Variant rs4715332 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 0.635 in 152,016 control chromosomes in the GnomAD database, including 31,274 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 0.64 ( 31274 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.22

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=-0.97).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.852 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:

0.635

AC:

96484

AN:

151898

Hom.:

31253

Cov.:

show subpopulations

Gnomad AFR

AF:

0.701

Gnomad AMI

AF:

0.659

Gnomad AMR

AF:

0.701

Gnomad ASJ

AF:

0.569

Gnomad EAS

AF:

0.874

Gnomad SAS

AF:

0.659

Gnomad FIN

AF:

0.564

Gnomad MID

AF:

0.601

Gnomad NFE

AF:

0.575

Gnomad OTH

AF:

0.630

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

GnomAD4 genome

AF:

0.635

AC:

96553

AN:

152016

Hom.:

31274

Cov.:

AF XY:

0.638

AC XY:

47429

AN XY:

74294

show subpopulations

Gnomad4 AFR

AF:

0.701

Gnomad4 AMR

AF:

0.701

Gnomad4 ASJ

AF:

0.569

Gnomad4 EAS

AF:

0.873

Gnomad4 SAS

AF:

0.658

Gnomad4 FIN

AF:

0.564

Gnomad4 NFE

AF:

0.575

Gnomad4 OTH

AF:

0.634

Alfa

AF:

0.589

Hom.:

45417

Bravo

AF:

0.648

Asia WGS

AF:

0.741

AC:

2576

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.11

DANN

Benign

0.31

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