Variant rs2495774 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 0.625 in 152,156 control chromosomes in the GnomAD database, including 32,252 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 0.63 ( 32252 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.28

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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.881 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:

0.625

AC:

95017

AN:

152038

Hom.:

32205

Cov.:

show subpopulations

Gnomad AFR

AF:

0.889

Gnomad AMI

AF:

0.567

Gnomad AMR

AF:

0.637

Gnomad ASJ

AF:

0.502

Gnomad EAS

AF:

0.802

Gnomad SAS

AF:

0.646

Gnomad FIN

AF:

0.445

Gnomad MID

AF:

0.734

Gnomad NFE

AF:

0.481

Gnomad OTH

AF:

0.638

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

GnomAD4 genome

AF:

0.625

AC:

95119

AN:

152156

Hom.:

32252

Cov.:

AF XY:

0.626

AC XY:

46574

AN XY:

74360

show subpopulations

Gnomad4 AFR

AF:

0.889

Gnomad4 AMR

AF:

0.637

Gnomad4 ASJ

AF:

0.502

Gnomad4 EAS

AF:

0.801

Gnomad4 SAS

AF:

0.646

Gnomad4 FIN

AF:

0.445

Gnomad4 NFE

AF:

0.481

Gnomad4 OTH

AF:

0.636

Alfa

AF:

0.517

Hom.:

28526

Bravo

AF:

0.654

Asia WGS

AF:

0.671

AC:

2327

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.0010

DANN

Benign

0.61

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