Variant rs4921583 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 0.559 in 151,990 control chromosomes in the GnomAD database, including 23,845 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 0.56 ( 23845 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.27

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=-1.05).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.573 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:

0.559

AC:

84928

AN:

151872

Hom.:

23802

Cov.:

show subpopulations

Gnomad AFR

AF:

0.579

Gnomad AMI

AF:

0.435

Gnomad AMR

AF:

0.533

Gnomad ASJ

AF:

0.602

Gnomad EAS

AF:

0.495

Gnomad SAS

AF:

0.537

Gnomad FIN

AF:

0.494

Gnomad MID

AF:

0.604

Gnomad NFE

AF:

0.569

Gnomad OTH

AF:

0.552

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

GnomAD4 genome

AF:

0.559

AC:

85029

AN:

151990

Hom.:

23845

Cov.:

AF XY:

0.554

AC XY:

41168

AN XY:

74288

show subpopulations

Gnomad4 AFR

AF:

0.580

Gnomad4 AMR

AF:

0.533

Gnomad4 ASJ

AF:

0.602

Gnomad4 EAS

AF:

0.496

Gnomad4 SAS

AF:

0.539

Gnomad4 FIN

AF:

0.494

Gnomad4 NFE

AF:

0.569

Gnomad4 OTH

AF:

0.555

Alfa

AF:

0.418

Hom.:

1026

Bravo

AF:

0.561

Asia WGS

AF:

0.500

AC:

1739

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.1

CADD

Benign

0.21

DANN

Benign

0.42

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