Variant rs2463226 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 0.547 in 152,002 control chromosomes in the GnomAD database, including 23,053 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 0.55 ( 23053 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.700

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=-0.99).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.764 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:

0.547

AC:

83068

AN:

151884

Hom.:

23030

Cov.:

show subpopulations

Gnomad AFR

AF:

0.541

Gnomad AMI

AF:

0.416

Gnomad AMR

AF:

0.559

Gnomad ASJ

AF:

0.525

Gnomad EAS

AF:

0.783

Gnomad SAS

AF:

0.722

Gnomad FIN

AF:

0.523

Gnomad MID

AF:

0.589

Gnomad NFE

AF:

0.524

Gnomad OTH

AF:

0.532

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

GnomAD4 genome

AF:

0.547

AC:

83123

AN:

152002

Hom.:

23053

Cov.:

AF XY:

0.551

AC XY:

40920

AN XY:

74282

show subpopulations

Gnomad4 AFR

AF:

0.541

Gnomad4 AMR

AF:

0.559

Gnomad4 ASJ

AF:

0.525

Gnomad4 EAS

AF:

0.784

Gnomad4 SAS

AF:

0.722

Gnomad4 FIN

AF:

0.523

Gnomad4 NFE

AF:

0.524

Gnomad4 OTH

AF:

0.534

Alfa

AF:

0.523

Hom.:

2497

Bravo

AF:

0.549

Asia WGS

AF:

0.737

AC:

2550

AN:

3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

1.4

DANN

Benign

0.33

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