rs7815788

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.159 in 152,056 control chromosomes in the GnomAD database, including 1,981 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.16 ( 1981 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.13

Publications

17 publications found
Variant links:

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ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.159
AC:
24105
AN:
151938
Hom.:
1976
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.211
Gnomad AMI
AF:
0.122
Gnomad AMR
AF:
0.162
Gnomad ASJ
AF:
0.193
Gnomad EAS
AF:
0.0603
Gnomad SAS
AF:
0.139
Gnomad FIN
AF:
0.133
Gnomad MID
AF:
0.155
Gnomad NFE
AF:
0.137
Gnomad OTH
AF:
0.176
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.159
AC:
24127
AN:
152056
Hom.:
1981
Cov.:
32
AF XY:
0.157
AC XY:
11661
AN XY:
74374
show subpopulations
African (AFR)
AF:
0.212
AC:
8773
AN:
41474
American (AMR)
AF:
0.162
AC:
2472
AN:
15280
Ashkenazi Jewish (ASJ)
AF:
0.193
AC:
670
AN:
3470
East Asian (EAS)
AF:
0.0601
AC:
311
AN:
5178
South Asian (SAS)
AF:
0.138
AC:
665
AN:
4810
European-Finnish (FIN)
AF:
0.133
AC:
1403
AN:
10580
Middle Eastern (MID)
AF:
0.150
AC:
44
AN:
294
European-Non Finnish (NFE)
AF:
0.137
AC:
9310
AN:
67956
Other (OTH)
AF:
0.175
AC:
368
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
1013
2025
3038
4050
5063
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
264
528
792
1056
1320
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.144
Hom.:
7573
Bravo
AF:
0.164
Asia WGS
AF:
0.133
AC:
463
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
2.8
DANN
Benign
0.73
PhyloP100
-1.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs7815788; hg19: chr8-57179020; API