Variant rs6937840 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 0.542 in 152,126 control chromosomes in the GnomAD database, including 22,782 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 0.54 ( 22782 hom., cov: 33)

Exomes 𝑓: 0.38 ( 0 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.46

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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.765 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:

0.542

AC:

82429

AN:

152000

Hom.:

22745

Cov.:

show subpopulations

Gnomad AFR

AF:

0.625

Gnomad AMI

AF:

0.673

Gnomad AMR

AF:

0.470

Gnomad ASJ

AF:

0.499

Gnomad EAS

AF:

0.785

Gnomad SAS

AF:

0.483

Gnomad FIN

AF:

0.486

Gnomad MID

AF:

0.506

Gnomad NFE

AF:

0.504

Gnomad OTH

AF:

0.539

GnomAD4 exome

AF:

0.375

AC:

AN:

Hom.:

AF XY:

0.375

AC XY:

AN XY:

show subpopulations

Gnomad4 FIN exome

AF:

0.250

Gnomad4 NFE exome

AF:

0.500

GnomAD4 genome

AF:

0.542

AC:

82511

AN:

152118

Hom.:

22782

Cov.:

AF XY:

0.540

AC XY:

40179

AN XY:

74368

show subpopulations

Gnomad4 AFR

AF:

0.625

Gnomad4 AMR

AF:

0.470

Gnomad4 ASJ

AF:

0.499

Gnomad4 EAS

AF:

0.785

Gnomad4 SAS

AF:

0.481

Gnomad4 FIN

AF:

0.486

Gnomad4 NFE

AF:

0.504

Gnomad4 OTH

AF:

0.541

Alfa

AF:

0.525

Hom.:

2633

Bravo

AF:

0.552

Asia WGS

AF:

0.628

AC:

2184

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.0080

DANN

Benign

0.19

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