rs6937815

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.0649 in 152,070 control chromosomes in the GnomAD database, including 692 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 0.065 ( 692 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.545
Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.0649
AC:
9868
AN:
151952
Hom.:
695
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0400
Gnomad AMI
AF:
0.0187
Gnomad AMR
AF:
0.136
Gnomad ASJ
AF:
0.0646
Gnomad EAS
AF:
0.392
Gnomad SAS
AF:
0.0328
Gnomad FIN
AF:
0.0287
Gnomad MID
AF:
0.0918
Gnomad NFE
AF:
0.0477
Gnomad OTH
AF:
0.0695
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0649
AC:
9872
AN:
152070
Hom.:
692
Cov.:
32
AF XY:
0.0677
AC XY:
5029
AN XY:
74336
show subpopulations
Gnomad4 AFR
AF:
0.0400
Gnomad4 AMR
AF:
0.136
Gnomad4 ASJ
AF:
0.0646
Gnomad4 EAS
AF:
0.393
Gnomad4 SAS
AF:
0.0326
Gnomad4 FIN
AF:
0.0287
Gnomad4 NFE
AF:
0.0477
Gnomad4 OTH
AF:
0.0693
Alfa
AF:
0.0203
Hom.:
23
Bravo
AF:
0.0750
Asia WGS
AF:
0.169
AC:
587
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
CADD
Benign
2.0
DANN
Benign
0.40

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: rs6937815; hg19: chr6-132745963; API