COL5A2 : c.568-10G>A

COL5A2 gene summary

Variant Details

Variant (CDS)Variant (protein)Variant Type Variant EffectGenomic Location (GRCh37)ExAC Frequency
c.568-10G>Asubstitutionsplice site chr2:189953508 (reverse strand)0.14129234

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.14129234 (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
ExAC0.15226060
10157 / 66708		0.09538966
989 / 10368		0.09618497
832 / 8650		0.18316172
3024 / 16510		0.09130961
1057 / 11576		0.13857791
916 / 6610		0.18502203
168 / 908		0.14129234
17143 / 121330
ESP 0.00000
0 / 8600		 0.00000
0 / 4400		 0.00000
0 / 13000
1KG
 0.17079
138 / 808		 0.08850
117 / 1322		 0.10615
107 / 1008		 0.17996
176 / 978		 0.12680
88 / 694		 0.15152
30 / 198		 0.13099
656 / 5008
View sub-population details for 1000 Genomes (1KG) data
Hide sub-population details for 1000 Genomes (1KG) data

0.13187
24 / 182
British
0.09016
11 / 122
African-American
0.13441
25 / 186
Chinese Dai
0.19186
33 / 172
Bengali
0.12766
24 / 188
Colombian
0.21028
45 / 214
Iberian
0.09375
18 / 192
African-Caribbean
0.08738
18 / 206
Han, Beijing
0.13592
28 / 206
Gujarati Indian
0.05469
7 / 128
Mexican, LA
0.15888
34 / 214
Toscani
0.07071
14 / 198
Esan, Nigeria
0.12981
27 / 208
Japanese
0.17157
35 / 204
Indian Telugu
0.11765
20 / 170
Peruvian
0.17677
35 / 198
Utah Europeans
0.11504
26 / 226
Gambian
0.10606
21 / 198
Kinh, Vietnam
0.22396
43 / 192
Punjabi, Lahore
0.17788
37 / 208
Puerto Rican
0.10101
20 / 198
Luhya, Kenya
0.07619
16 / 210
Southern Han
0.18137
37 / 204
Tamil
0.09412
16 / 170
Mende
0.05556
12 / 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 ENST00000374866 NM_000393.3
Protein ENSP00000364000 P05997



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.