Variant rs2444769 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 0.669 in 151,808 control chromosomes in the GnomAD database, including 37,512 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 ( 37512 hom., cov: 30)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.668

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=-0.86).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.822 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:

0.670

AC:

101566

AN:

151688

Hom.:

37497

Cov.:

show subpopulations

Gnomad AFR

AF:

0.331

Gnomad AMI

AF:

0.944

Gnomad AMR

AF:

0.765

Gnomad ASJ

AF:

0.715

Gnomad EAS

AF:

0.844

Gnomad SAS

AF:

0.807

Gnomad FIN

AF:

0.860

Gnomad MID

AF:

0.646

Gnomad NFE

AF:

0.795

Gnomad OTH

AF:

0.666

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

GnomAD4 genome

AF:

0.669

AC:

101598

AN:

151808

Hom.:

37512

Cov.:

AF XY:

0.679

AC XY:

50394

AN XY:

74192

show subpopulations

Gnomad4 AFR

AF:

0.331

Gnomad4 AMR

AF:

0.765

Gnomad4 ASJ

AF:

0.715

Gnomad4 EAS

AF:

0.843

Gnomad4 SAS

AF:

0.808

Gnomad4 FIN

AF:

0.860

Gnomad4 NFE

AF:

0.795

Gnomad4 OTH

AF:

0.669

Alfa

AF:

0.775

Hom.:

22402

Bravo

AF:

0.644

Asia WGS

AF:

0.798

AC:

2762

AN:

3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

4.5

DANN

Benign

0.53

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