Variant rs277522 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 0.921 in 151,906 control chromosomes in the GnomAD database, including 64,465 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 0.92 ( 64465 hom., cov: 28)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.195

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=-0.93).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.946 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:

0.921

AC:

139752

AN:

151788

Hom.:

64414

Cov.:

show subpopulations

Gnomad AFR

AF:

0.925

Gnomad AMI

AF:

0.998

Gnomad AMR

AF:

0.885

Gnomad ASJ

AF:

0.839

Gnomad EAS

AF:

0.968

Gnomad SAS

AF:

0.881

Gnomad FIN

AF:

0.942

Gnomad MID

AF:

0.810

Gnomad NFE

AF:

0.926

Gnomad OTH

AF:

0.892

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

GnomAD4 genome

AF:

0.921

AC:

139858

AN:

151906

Hom.:

64465

Cov.:

AF XY:

0.920

AC XY:

68254

AN XY:

74220

show subpopulations

Gnomad4 AFR

AF:

0.925

Gnomad4 AMR

AF:

0.885

Gnomad4 ASJ

AF:

0.839

Gnomad4 EAS

AF:

0.968

Gnomad4 SAS

AF:

0.881

Gnomad4 FIN

AF:

0.942

Gnomad4 NFE

AF:

0.926

Gnomad4 OTH

AF:

0.893

Alfa

AF:

0.920

Hom.:

77739

Bravo

AF:

0.918

Asia WGS

AF:

0.939

AC:

3265

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

2.6

DANN

Benign

0.73

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