Variant rs917183 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 0.529 in 151,886 control chromosomes in the GnomAD database, including 21,746 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 0.53 ( 21746 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.669

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 (AFR) allele frequency at 95% confidence interval = 0.638 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:

0.529

AC:

80273

AN:

151768

Hom.:

21719

Cov.:

show subpopulations

Gnomad AFR

AF:

0.644

Gnomad AMI

AF:

0.299

Gnomad AMR

AF:

0.493

Gnomad ASJ

AF:

0.612

Gnomad EAS

AF:

0.556

Gnomad SAS

AF:

0.634

Gnomad FIN

AF:

0.395

Gnomad MID

AF:

0.677

Gnomad NFE

AF:

0.476

Gnomad OTH

AF:

0.556

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

GnomAD4 genome

AF:

0.529

AC:

80344

AN:

151886

Hom.:

21746

Cov.:

AF XY:

0.527

AC XY:

39089

AN XY:

74216

show subpopulations

Gnomad4 AFR

AF:

0.644

Gnomad4 AMR

AF:

0.492

Gnomad4 ASJ

AF:

0.612

Gnomad4 EAS

AF:

0.557

Gnomad4 SAS

AF:

0.635

Gnomad4 FIN

AF:

0.395

Gnomad4 NFE

AF:

0.476

Gnomad4 OTH

AF:

0.554

Alfa

AF:

0.521

Hom.:

3011

Bravo

AF:

0.541

Asia WGS

AF:

0.587

AC:

2041

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

3.1

DANN

Benign

0.41

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