Variant rs2476761 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 0.747 in 152,096 control chromosomes in the GnomAD database, including 42,596 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 0.75 ( 42596 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.956

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=-0.95).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.747

AC:

113583

AN:

151978

Hom.:

42554

Cov.:

show subpopulations

Gnomad AFR

AF:

0.724

Gnomad AMI

AF:

0.715

Gnomad AMR

AF:

0.765

Gnomad ASJ

AF:

0.822

Gnomad EAS

AF:

0.927

Gnomad SAS

AF:

0.771

Gnomad FIN

AF:

0.735

Gnomad MID

AF:

0.886

Gnomad NFE

AF:

0.739

Gnomad OTH

AF:

0.778

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.747

AC:

113677

AN:

152096

Hom.:

42596

Cov.:

AF XY:

0.750

AC XY:

55778

AN XY:

74356

show subpopulations

Gnomad4 AFR

AF:

0.724

Gnomad4 AMR

AF:

0.765

Gnomad4 ASJ

AF:

0.822

Gnomad4 EAS

AF:

0.927

Gnomad4 SAS

AF:

0.771

Gnomad4 FIN

AF:

0.735

Gnomad4 NFE

AF:

0.739

Gnomad4 OTH

AF:

0.777

Alfa

AF:

0.709

Hom.:

4241

Bravo

AF:

0.751

Asia WGS

AF:

0.831

AC:

2888

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.95

DANN

Benign

0.54

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