Variant rs4238010 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 0.832 in 152,182 control chromosomes in the GnomAD database, including 53,290 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 0.83 ( 53290 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.31

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=-0.94).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.918 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:

0.832

AC:

126497

AN:

152064

Hom.:

53254

Cov.:

show subpopulations

Gnomad AFR

AF:

0.691

Gnomad AMI

AF:

0.989

Gnomad AMR

AF:

0.919

Gnomad ASJ

AF:

0.905

Gnomad EAS

AF:

0.939

Gnomad SAS

AF:

0.928

Gnomad FIN

AF:

0.845

Gnomad MID

AF:

0.972

Gnomad NFE

AF:

0.873

Gnomad OTH

AF:

0.865

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

GnomAD4 genome

AF:

0.832

AC:

126586

AN:

152182

Hom.:

53290

Cov.:

AF XY:

0.834

AC XY:

62051

AN XY:

74402

show subpopulations

Gnomad4 AFR

AF:

0.691

Gnomad4 AMR

AF:

0.919

Gnomad4 ASJ

AF:

0.905

Gnomad4 EAS

AF:

0.940

Gnomad4 SAS

AF:

0.929

Gnomad4 FIN

AF:

0.845

Gnomad4 NFE

AF:

0.873

Gnomad4 OTH

AF:

0.867

Alfa

AF:

0.878

Hom.:

128952

Bravo

AF:

0.832

Asia WGS

AF:

0.924

AC:

3214

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.0040

DANN

Benign

0.38

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