SCN10A : c.1868-9A>G

SCN10A gene summary

Variant Details

Variant (CDS)Variant (protein)Variant Type Variant EffectGenomic Location (GRCh37)ExAC Frequency
c.1868-9A>Gsubstitutionsplice site chr3:38784029 (reverse strand)0.65368451

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.65368451 (ExAC mean allelic frequency), it is highly unlikely to be pathogenic.

Detection in Population Databases



Database European African East Asian South Asian American Finnish Other Total
ExAC0.59761221
39544 / 66170		0.90699273
9235 / 10182		0.85593023
7361 / 8600		0.64579530
10613 / 16434		0.67932893
7815 / 11504		0.54176755
3580 / 6608		0.61581292
553 / 898		0.65368451
78701 / 120396
ESP 0.00000
0 / 8600		 0.00000
0 / 4400		 0.00000
0 / 13000
1KG
 0.59530
481 / 808		 0.95008
1256 / 1322		 0.83730
844 / 1008		 0.68712
672 / 978		 0.62392
433 / 694		 0.55051
109 / 198		 0.75779
3795 / 5008
View sub-population details for 1000 Genomes (1KG) data
Hide sub-population details for 1000 Genomes (1KG) data

0.60440
110 / 182
British
0.89344
109 / 122
African-American
0.83871
156 / 186
Chinese Dai
0.67442
116 / 172
Bengali
0.55851
105 / 188
Colombian
0.58879
126 / 214
Iberian
0.93229
179 / 192
African-Caribbean
0.89320
184 / 206
Han, Beijing
0.66505
137 / 206
Gujarati Indian
0.69531
89 / 128
Mexican, LA
0.61215
131 / 214
Toscani
0.98990
196 / 198
Esan, Nigeria
0.81250
169 / 208
Japanese
0.68627
140 / 204
Indian Telugu
0.65294
111 / 170
Peruvian
0.57576
114 / 198
Utah Europeans
0.89823
203 / 226
Gambian
0.79798
158 / 198
Kinh, Vietnam
0.69271
133 / 192
Punjabi, Lahore
0.61538
128 / 208
Puerto Rican
0.95455
189 / 198
Luhya, Kenya
0.84286
177 / 210
Southern Han
0.71569
146 / 204
Tamil
0.97647
166 / 170
Mende
0.99074
214 / 216
Yoruba, Nigeria

The Exome Aggregation Consortium (ExAC) is a database of 60,706 unrelated individuals sequenced as part of various disease-specific and population genetic studies. There is partial overlap between ExAC and 1000 Genomes (1KG) (1,851 of the 2,504 samples in 1KG) and the Exome Sequencing Project (ESP) (3,936 of the 6,500 samples in ESP).


Other Variant & Gene Details

Canonical Sequences
Transcript ENST00000449082 NM_006514.2
Protein ENSP00000390600 Q9Y5Y9



References

1. Roddy Walsh, Kate L. Thomson, James S. Ware, Birgit H. Funke, Jessica Woodley, Karen J. McGuire, Francesco Mazzarotto, Edward Blair, Anneke Seller, Jenny C. Taylor, Eric V. Minikel, Exome Aggregation Consortium, Daniel G. MacArthur, Martin Farrall, Stuart A. Cook and Hugh Watkins. Reassessment of Mendelian gene pathogenicity using 7,855 cardiomyopathy cases and 60,706 reference samples. Genet Med. 2016 doi:10.1038/gim.2016.90.

2. Pugh TJ, Kelly MA, Gowrisankar S, Hynes E, Seidman MA, Baxter SM, Bowser M, Harrison B, Aaron D, Mahanta LM, Lakdawala NK, McDermott G, White ET, Rehm HL, Lebo M, Funke BH. The landscape of genetic variation in dilated cardiomyopathy as surveyed by clinical DNA sequencing. Genet Med. 2014 Aug;16(8):601-8.

3. Alfares AA, Kelly MA, McDermott G, Funke BH, Lebo MS, Baxter SB, Shen J, McLaughlin HM, Clark EH, Babb LJ, Cox SW, DePalma SR, Ho CY, Seidman JG, Seidman CE, Rehm HL. Results of clinical genetic testing of 2,912 probands with hypertrophic cardiomyopathy: expanded panels offer limited additional sensitivity. Genet Med. 2015 Nov;17(11):880-8.