Variant 7-63117392-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 0.793 in 227,688 control chromosomes in the GnomAD database, including 72,003 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 0.78 ( 47024 hom., cov: 32)

Exomes 𝑓: 0.81 ( 24979 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -5.51

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=-1.07).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.874 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:

0.783

AC:

119008

AN:

151940

Hom.:

46970

Cov.:

show subpopulations

Gnomad AFR

AF:

0.882

Gnomad AMI

AF:

0.604

Gnomad AMR

AF:

0.829

Gnomad ASJ

AF:

0.727

Gnomad EAS

AF:

0.778

Gnomad SAS

AF:

0.762

Gnomad FIN

AF:

0.775

Gnomad MID

AF:

0.739

Gnomad NFE

AF:

0.722

Gnomad OTH

AF:

0.768

GnomAD4 exome

AF:

0.812

AC:

61385

AN:

75630

Hom.:

24979

AF XY:

0.810

AC XY:

34602

AN XY:

42724

show subpopulations

Gnomad4 AFR exome

AF:

0.915

Gnomad4 AMR exome

AF:

0.893

Gnomad4 ASJ exome

AF:

0.804

Gnomad4 EAS exome

AF:

0.828

Gnomad4 SAS exome

AF:

0.828

Gnomad4 FIN exome

AF:

0.831

Gnomad4 NFE exome

AF:

0.797

Gnomad4 OTH exome

AF:

0.816

GnomAD4 genome

AF:

0.783

AC:

119119

AN:

152058

Hom.:

47024

Cov.:

AF XY:

0.786

AC XY:

58432

AN XY:

74338

show subpopulations

Gnomad4 AFR

AF:

0.882

Gnomad4 AMR

AF:

0.829

Gnomad4 ASJ

AF:

0.727

Gnomad4 EAS

AF:

0.778

Gnomad4 SAS

AF:

0.763

Gnomad4 FIN

AF:

0.775

Gnomad4 NFE

AF:

0.722

Gnomad4 OTH

AF:

0.768

Alfa

AF:

0.735

Hom.:

48717

Bravo

AF:

0.793

Asia WGS

AF:

0.786

AC:

2732

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

0.27

DANN

Benign

0.45

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