Variant 6-31520368-A-G 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 0.786 in 660,704 control chromosomes in the GnomAD database, including 205,350 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 ( 47761 hom., cov: 32)

Exomes 𝑓: 0.78 ( 157589 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.769

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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.878 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:

0.791

AC:

120286

AN:

151980

Hom.:

47720

Cov.:

show subpopulations

Gnomad AFR

AF:

0.822

Gnomad AMI

AF:

0.669

Gnomad AMR

AF:

0.811

Gnomad ASJ

AF:

0.859

Gnomad EAS

AF:

0.899

Gnomad SAS

AF:

0.860

Gnomad FIN

AF:

0.810

Gnomad MID

AF:

0.864

Gnomad NFE

AF:

0.751

Gnomad OTH

AF:

0.787

GnomAD4 exome

AF:

0.784

AC:

398684

AN:

508606

Hom.:

157589

AF XY:

0.789

AC XY:

214029

AN XY:

271214

show subpopulations

Gnomad4 AFR exome

AF:

0.824

Gnomad4 AMR exome

AF:

0.805

Gnomad4 ASJ exome

AF:

0.855

Gnomad4 EAS exome

AF:

0.901

Gnomad4 SAS exome

AF:

0.869

Gnomad4 FIN exome

AF:

0.795

Gnomad4 NFE exome

AF:

0.749

Gnomad4 OTH exome

AF:

0.775

GnomAD4 genome

AF:

0.791

AC:

120380

AN:

152098

Hom.:

47761

Cov.:

AF XY:

0.797

AC XY:

59268

AN XY:

74336

show subpopulations

Gnomad4 AFR

AF:

0.821

Gnomad4 AMR

AF:

0.812

Gnomad4 ASJ

AF:

0.859

Gnomad4 EAS

AF:

0.899

Gnomad4 SAS

AF:

0.861

Gnomad4 FIN

AF:

0.810

Gnomad4 NFE

AF:

0.751

Gnomad4 OTH

AF:

0.789

Alfa

AF:

0.768

Hom.:

74420

Bravo

AF:

0.792

Asia WGS

AF:

0.823

AC:

2864

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.028

DANN

Benign

0.39

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