Variant rs10777629 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 0.821 in 152,126 control chromosomes in the GnomAD database, including 51,341 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 0.82 ( 51341 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.657

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=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.872 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:

0.821

AC:

124795

AN:

152008

Hom.:

51282

Cov.:

show subpopulations

Gnomad AFR

AF:

0.831

Gnomad AMI

AF:

0.759

Gnomad AMR

AF:

0.884

Gnomad ASJ

AF:

0.783

Gnomad EAS

AF:

0.892

Gnomad SAS

AF:

0.802

Gnomad FIN

AF:

0.850

Gnomad MID

AF:

0.775

Gnomad NFE

AF:

0.795

Gnomad OTH

AF:

0.828

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

GnomAD4 genome

AF:

0.821

AC:

124915

AN:

152126

Hom.:

51341

Cov.:

AF XY:

0.826

AC XY:

61390

AN XY:

74348

show subpopulations

Gnomad4 AFR

AF:

0.831

Gnomad4 AMR

AF:

0.884

Gnomad4 ASJ

AF:

0.783

Gnomad4 EAS

AF:

0.891

Gnomad4 SAS

AF:

0.801

Gnomad4 FIN

AF:

0.850

Gnomad4 NFE

AF:

0.795

Gnomad4 OTH

AF:

0.829

Alfa

AF:

0.801

Hom.:

98483

Bravo

AF:

0.825

Asia WGS

AF:

0.854

AC:

2969

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

7.1

DANN

Benign

0.67

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