Variant rs1467142 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 0.913 in 151,046 control chromosomes in the GnomAD database, including 63,354 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 0.91 ( 63354 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.01

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 (NFE) allele frequency at 95% confidence interval = 0.938 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:

0.913

AC:

137791

AN:

150930

Hom.:

63322

Cov.:

show subpopulations

Gnomad AFR

AF:

0.857

Gnomad AMI

AF:

0.986

Gnomad AMR

AF:

0.885

Gnomad ASJ

AF:

0.970

Gnomad EAS

AF:

0.923

Gnomad SAS

AF:

0.890

Gnomad FIN

AF:

0.943

Gnomad MID

AF:

0.962

Gnomad NFE

AF:

0.944

Gnomad OTH

AF:

0.928

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

GnomAD4 genome

AF:

0.913

AC:

137877

AN:

151046

Hom.:

63354

Cov.:

AF XY:

0.911

AC XY:

67269

AN XY:

73806

show subpopulations

Gnomad4 AFR

AF:

0.857

Gnomad4 AMR

AF:

0.885

Gnomad4 ASJ

AF:

0.970

Gnomad4 EAS

AF:

0.923

Gnomad4 SAS

AF:

0.891

Gnomad4 FIN

AF:

0.943

Gnomad4 NFE

AF:

0.944

Gnomad4 OTH

AF:

0.929

Alfa

AF:

0.908

Hom.:

3922

Bravo

AF:

0.907

Asia WGS

AF:

0.909

AC:

3163

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

3.5

DANN

Benign

0.54

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