rs3759916

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 0.962 in 152,382 control chromosomes in the GnomAD database, including 70,963 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 0.96 ( 70963 hom., cov: 35)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.114
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=-0.76).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.989 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:
0.962
AC:
146549
AN:
152264
Hom.:
70916
Cov.:
35
show subpopulations
Gnomad AFR
AF:
0.970
Gnomad AMI
AF:
1.00
Gnomad AMR
AF:
0.883
Gnomad ASJ
AF:
0.995
Gnomad EAS
AF:
0.651
Gnomad SAS
AF:
0.929
Gnomad FIN
AF:
0.995
Gnomad MID
AF:
0.984
Gnomad NFE
AF:
0.995
Gnomad OTH
AF:
0.961
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.962
AC:
146655
AN:
152382
Hom.:
70963
Cov.:
35
AF XY:
0.958
AC XY:
71395
AN XY:
74514
show subpopulations
Gnomad4 AFR
AF:
0.969
AC:
0.969492
AN:
0.969492
Gnomad4 AMR
AF:
0.883
AC:
0.882772
AN:
0.882772
Gnomad4 ASJ
AF:
0.995
AC:
0.995392
AN:
0.995392
Gnomad4 EAS
AF:
0.652
AC:
0.651662
AN:
0.651662
Gnomad4 SAS
AF:
0.929
AC:
0.928808
AN:
0.928808
Gnomad4 FIN
AF:
0.995
AC:
0.994731
AN:
0.994731
Gnomad4 NFE
AF:
0.995
AC:
0.994812
AN:
0.994812
Gnomad4 OTH
AF:
0.959
AC:
0.959357
AN:
0.959357
Heterozygous variant carriers
0
246
492
739
985
1231
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
908
1816
2724
3632
4540
<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:
0.982
Hom.:
33929
Bravo
AF:
0.953
Asia WGS
AF:
0.804
AC:
2798
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.76
CADD
Benign
11
DANN
Benign
0.78

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs3759916; hg19: chr15-92936169; API