Variant rs2652485 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 0.674 in 151,980 control chromosomes in the GnomAD database, including 35,355 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 0.67 ( 35355 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.176

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=-0.95).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.796 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:

0.674

AC:

102306

AN:

151862

Hom.:

35308

Cov.:

show subpopulations

Gnomad AFR

AF:

0.803

Gnomad AMI

AF:

0.584

Gnomad AMR

AF:

0.527

Gnomad ASJ

AF:

0.539

Gnomad EAS

AF:

0.603

Gnomad SAS

AF:

0.475

Gnomad FIN

AF:

0.696

Gnomad MID

AF:

0.544

Gnomad NFE

AF:

0.653

Gnomad OTH

AF:

0.652

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

GnomAD4 genome

AF:

0.674

AC:

102403

AN:

151980

Hom.:

35355

Cov.:

AF XY:

0.667

AC XY:

49552

AN XY:

74262

show subpopulations

Gnomad4 AFR

AF:

0.803

Gnomad4 AMR

AF:

0.527

Gnomad4 ASJ

AF:

0.539

Gnomad4 EAS

AF:

0.603

Gnomad4 SAS

AF:

0.475

Gnomad4 FIN

AF:

0.696

Gnomad4 NFE

AF:

0.653

Gnomad4 OTH

AF:

0.656

Alfa

AF:

0.670

Hom.:

4294

Bravo

AF:

0.668

Asia WGS

AF:

0.601

AC:

2090

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.85

DANN

Benign

0.55

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