TSC2 : c.482-3C>T

TSC2 gene summary

Variant Details

Variant (CDS)Variant (protein)Variant Type Variant EffectGenomic Location (GRCh37)ExAC Frequency
c.482-3C>Tsubstitutionsplice site chr16:2105400 (forward strand)0.08710623

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.08710623 (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
ExAC0.09807565
6544 / 66724		0.20161445
2098 / 10406		0.00000000
0 / 8654		0.02489400
411 / 16510		0.04880788
565 / 11576		0.13078319
865 / 6614		0.10022026
91 / 908		0.08710623
10574 / 121392
ESP 0.09663
831 / 8600		 0.19063
838 / 4396		 0.12842
1669 / 12996
1KG
 0.08787
71 / 808		 0.20802
275 / 1322		 0.00000
0 / 1008		 0.02147
21 / 978		 0.09366
65 / 694		 0.14646
29 / 198		 0.09205
461 / 5008
View sub-population details for 1000 Genomes (1KG) data
Hide sub-population details for 1000 Genomes (1KG) data

0.05495
10 / 182
British
0.13934
17 / 122
African-American
0.00000
0 / 186
Chinese Dai
0.02326
4 / 172
Bengali
0.11170
21 / 188
Colombian
0.12150
26 / 214
Iberian
0.20312
39 / 192
African-Caribbean
0.00000
0 / 206
Han, Beijing
0.01942
4 / 206
Gujarati Indian
0.08594
11 / 128
Mexican, LA
0.08879
19 / 214
Toscani
0.22222
44 / 198
Esan, Nigeria
0.00000
0 / 208
Japanese
0.03431
7 / 204
Indian Telugu
0.05294
9 / 170
Peruvian
0.08081
16 / 198
Utah Europeans
0.23894
54 / 226
Gambian
0.00000
0 / 198
Kinh, Vietnam
0.00000
0 / 192
Punjabi, Lahore
0.11538
24 / 208
Puerto Rican
0.20202
40 / 198
Luhya, Kenya
0.00000
0 / 210
Southern Han
0.02941
6 / 204
Tamil
0.22941
39 / 170
Mende
0.19444
42 / 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.