Variant rs6937815 details in Genebe, Genetics Data Aggregator

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

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.:

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.:

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.:

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over