Variant rs2254191 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 0.579 in 151,556 control chromosomes in the GnomAD database, including 27,084 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 0.58 ( 27084 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.47

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 (EAS) allele frequency at 95% confidence interval = 0.784 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:

0.580

AC:

87758

AN:

151434

Hom.:

27087

Cov.:

show subpopulations

Gnomad AFR

AF:

0.356

Gnomad AMI

AF:

0.538

Gnomad AMR

AF:

0.544

Gnomad ASJ

AF:

0.606

Gnomad EAS

AF:

0.805

Gnomad SAS

AF:

0.683

Gnomad FIN

AF:

0.694

Gnomad MID

AF:

0.640

Gnomad NFE

AF:

0.680

Gnomad OTH

AF:

0.594

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

GnomAD4 genome

AF:

0.579

AC:

87784

AN:

151556

Hom.:

27084

Cov.:

AF XY:

0.581

AC XY:

43034

AN XY:

74062

show subpopulations

Gnomad4 AFR

AF:

0.356

Gnomad4 AMR

AF:

0.544

Gnomad4 ASJ

AF:

0.606

Gnomad4 EAS

AF:

0.805

Gnomad4 SAS

AF:

0.683

Gnomad4 FIN

AF:

0.694

Gnomad4 NFE

AF:

0.680

Gnomad4 OTH

AF:

0.595

Alfa

AF:

0.652

Hom.:

30546

Bravo

AF:

0.559

Asia WGS

AF:

0.725

AC:

2519

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

0.0040

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