Variant rs391763 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 0.654 in 151,270 control chromosomes in the GnomAD database, including 32,485 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 0.65 ( 32485 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.250

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=-0.85).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.802 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:

0.654

AC:

98900

AN:

151154

Hom.:

32487

Cov.:

show subpopulations

Gnomad AFR

AF:

0.645

Gnomad AMI

AF:

0.613

Gnomad AMR

AF:

0.701

Gnomad ASJ

AF:

0.749

Gnomad EAS

AF:

0.823

Gnomad SAS

AF:

0.588

Gnomad FIN

AF:

0.581

Gnomad MID

AF:

0.726

Gnomad NFE

AF:

0.648

Gnomad OTH

AF:

0.673

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

GnomAD4 genome

AF:

0.654

AC:

98928

AN:

151270

Hom.:

32485

Cov.:

AF XY:

0.649

AC XY:

47965

AN XY:

73850

show subpopulations

Gnomad4 AFR

AF:

0.644

Gnomad4 AMR

AF:

0.701

Gnomad4 ASJ

AF:

0.749

Gnomad4 EAS

AF:

0.823

Gnomad4 SAS

AF:

0.587

Gnomad4 FIN

AF:

0.581

Gnomad4 NFE

AF:

0.648

Gnomad4 OTH

AF:

0.671

Alfa

AF:

0.638

Hom.:

3714

Bravo

AF:

0.671

Asia WGS

AF:

0.633

AC:

2198

AN:

3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.36

DANN

Benign

0.23

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