Variant rs6131295 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 0.79 in 150,020 control chromosomes in the GnomAD database, including 47,047 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 0.79 ( 47047 hom., cov: 26)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.452

Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.842 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:

0.790

AC:

118394

AN:

149916

Hom.:

46996

Cov.:

show subpopulations

Gnomad AFR

AF:

0.849

Gnomad AMI

AF:

0.808

Gnomad AMR

AF:

0.828

Gnomad ASJ

AF:

0.822

Gnomad EAS

AF:

0.776

Gnomad SAS

AF:

0.773

Gnomad FIN

AF:

0.784

Gnomad MID

AF:

0.811

Gnomad NFE

AF:

0.747

Gnomad OTH

AF:

0.794

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

GnomAD4 genome

AF:

0.790

AC:

118498

AN:

150020

Hom.:

47047

Cov.:

AF XY:

0.792

AC XY:

57841

AN XY:

73060

show subpopulations

Gnomad4 AFR

AF:

0.849

Gnomad4 AMR

AF:

0.828

Gnomad4 ASJ

AF:

0.822

Gnomad4 EAS

AF:

0.777

Gnomad4 SAS

AF:

0.773

Gnomad4 FIN

AF:

0.784

Gnomad4 NFE

AF:

0.747

Gnomad4 OTH

AF:

0.795

Alfa

AF:

0.758

Hom.:

86749

Bravo

AF:

0.800

Asia WGS

AF:

0.798

AC:

2776

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

1.4

DANN

Benign

0.22

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