Variant rs964293 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 0.433 in 151,850 control chromosomes in the GnomAD database, including 14,958 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 0.43 ( 14958 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0950

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=-0.96).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.63 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:

0.433

AC:

65642

AN:

151732

Hom.:

14937

Cov.:

show subpopulations

Gnomad AFR

AF:

0.556

Gnomad AMI

AF:

0.276

Gnomad AMR

AF:

0.417

Gnomad ASJ

AF:

0.455

Gnomad EAS

AF:

0.647

Gnomad SAS

AF:

0.407

Gnomad FIN

AF:

0.314

Gnomad MID

AF:

0.446

Gnomad NFE

AF:

0.365

Gnomad OTH

AF:

0.448

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

GnomAD4 genome

AF:

0.433

AC:

65707

AN:

151850

Hom.:

14958

Cov.:

AF XY:

0.432

AC XY:

32018

AN XY:

74200

show subpopulations

Gnomad4 AFR

AF:

0.556

Gnomad4 AMR

AF:

0.417

Gnomad4 ASJ

AF:

0.455

Gnomad4 EAS

AF:

0.648

Gnomad4 SAS

AF:

0.405

Gnomad4 FIN

AF:

0.314

Gnomad4 NFE

AF:

0.365

Gnomad4 OTH

AF:

0.449

Alfa

AF:

0.382

Hom.:

23348

Bravo

AF:

0.447

Asia WGS

AF:

0.512

AC:

1776

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.47

DANN

Benign

0.51

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