TSC2 : c.5161-10A>C

TSC2 gene summary

Variant Details

Variant (CDS)Variant (protein)Variant Type Variant EffectGenomic Location (GRCh37)ExAC Frequency
c.5161-10A>Csubstitutionsplice site chr16:2138218 (forward strand)0.20671736

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.20671736 (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
ExAC0.21662270
14288 / 65958		0.56233036
5801 / 10316		0.00034779
3 / 8626		0.09687386
1599 / 16506		0.11238095
1298 / 11550		0.25922565
1714 / 6612		0.22209821
199 / 896		0.20671736
24902 / 120464
ESP 0.00000
0 / 8600		 0.00000
0 / 4400		 0.00000
0 / 13000
1KG
 0.22030
178 / 808		 0.61573
814 / 1322		 0.00000
0 / 1008		 0.08998
88 / 978		 0.21326
148 / 694		 0.29798
59 / 198		 0.25699
1287 / 5008
View sub-population details for 1000 Genomes (1KG) data
Hide sub-population details for 1000 Genomes (1KG) data

0.19780
36 / 182
British
0.46721
57 / 122
African-American
0.00000
0 / 186
Chinese Dai
0.06977
12 / 172
Bengali
0.28723
54 / 188
Colombian
0.23832
51 / 214
Iberian
0.64062
123 / 192
African-Caribbean
0.00000
0 / 206
Han, Beijing
0.10680
22 / 206
Gujarati Indian
0.16406
21 / 128
Mexican, LA
0.22897
49 / 214
Toscani
0.64646
128 / 198
Esan, Nigeria
0.00000
0 / 208
Japanese
0.11275
23 / 204
Indian Telugu
0.09412
16 / 170
Peruvian
0.21212
42 / 198
Utah Europeans
0.62389
141 / 226
Gambian
0.00000
0 / 198
Kinh, Vietnam
0.07292
14 / 192
Punjabi, Lahore
0.27404
57 / 208
Puerto Rican
0.60606
120 / 198
Luhya, Kenya
0.00000
0 / 210
Southern Han
0.08333
17 / 204
Tamil
0.65294
111 / 170
Mende
0.62037
134 / 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 ENST00000219476 NM_000548.3
Protein ENSP00000219476 P49815



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.