Variant rs393974 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 0.619 in 152,032 control chromosomes in the GnomAD database, including 29,443 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 0.62 ( 29443 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.229

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=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.789 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:

0.619

AC:

94024

AN:

151914

Hom.:

29399

Cov.:

show subpopulations

Gnomad AFR

AF:

0.603

Gnomad AMI

AF:

0.738

Gnomad AMR

AF:

0.699

Gnomad ASJ

AF:

0.655

Gnomad EAS

AF:

0.810

Gnomad SAS

AF:

0.610

Gnomad FIN

AF:

0.557

Gnomad MID

AF:

0.582

Gnomad NFE

AF:

0.603

Gnomad OTH

AF:

0.618

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

GnomAD4 genome

AF:

0.619

AC:

94129

AN:

152032

Hom.:

29443

Cov.:

AF XY:

0.619

AC XY:

45981

AN XY:

74312

show subpopulations

Gnomad4 AFR

AF:

0.603

Gnomad4 AMR

AF:

0.700

Gnomad4 ASJ

AF:

0.655

Gnomad4 EAS

AF:

0.810

Gnomad4 SAS

AF:

0.610

Gnomad4 FIN

AF:

0.557

Gnomad4 NFE

AF:

0.603

Gnomad4 OTH

AF:

0.619

Alfa

AF:

0.525

Hom.:

1579

Bravo

AF:

0.631

Asia WGS

AF:

0.697

AC:

2424

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.92

DANN

Benign

0.63

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