Variant rs2451563 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 0.459 in 151,890 control chromosomes in the GnomAD database, including 19,786 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 0.46 ( 19786 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0240

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 (NFE) allele frequency at 95% confidence interval = 0.621 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:

0.459

AC:

69672

AN:

151770

Hom.:

19778

Cov.:

show subpopulations

Gnomad AFR

AF:

0.115

Gnomad AMI

AF:

0.720

Gnomad AMR

AF:

0.512

Gnomad ASJ

AF:

0.690

Gnomad EAS

AF:

0.415

Gnomad SAS

AF:

0.551

Gnomad FIN

AF:

0.534

Gnomad MID

AF:

0.532

Gnomad NFE

AF:

0.625

Gnomad OTH

AF:

0.494

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

GnomAD4 genome

AF:

0.459

AC:

69694

AN:

151890

Hom.:

19786

Cov.:

AF XY:

0.456

AC XY:

33869

AN XY:

74228

show subpopulations

Gnomad4 AFR

AF:

0.114

Gnomad4 AMR

AF:

0.512

Gnomad4 ASJ

AF:

0.690

Gnomad4 EAS

AF:

0.417

Gnomad4 SAS

AF:

0.551

Gnomad4 FIN

AF:

0.534

Gnomad4 NFE

AF:

0.626

Gnomad4 OTH

AF:

0.499

Alfa

AF:

0.523

Hom.:

2847

Bravo

AF:

0.446

Asia WGS

AF:

0.429

AC:

1495

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

2.2

DANN

Benign

0.50

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