Variant rs442432 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 0.771 in 152,112 control chromosomes in the GnomAD database, including 45,873 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 0.77 ( 45873 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.679

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=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.894 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:

0.771

AC:

117193

AN:

151994

Hom.:

45837

Cov.:

show subpopulations

Gnomad AFR

AF:

0.902

Gnomad AMI

AF:

0.706

Gnomad AMR

AF:

0.703

Gnomad ASJ

AF:

0.714

Gnomad EAS

AF:

0.622

Gnomad SAS

AF:

0.762

Gnomad FIN

AF:

0.669

Gnomad MID

AF:

0.794

Gnomad NFE

AF:

0.739

Gnomad OTH

AF:

0.749

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

GnomAD4 genome

AF:

0.771

AC:

117277

AN:

152112

Hom.:

45873

Cov.:

AF XY:

0.766

AC XY:

56917

AN XY:

74338

show subpopulations

Gnomad4 AFR

AF:

0.902

Gnomad4 AMR

AF:

0.703

Gnomad4 ASJ

AF:

0.714

Gnomad4 EAS

AF:

0.622

Gnomad4 SAS

AF:

0.761

Gnomad4 FIN

AF:

0.669

Gnomad4 NFE

AF:

0.739

Gnomad4 OTH

AF:

0.745

Alfa

AF:

0.738

Hom.:

79434

Bravo

AF:

0.776

Asia WGS

AF:

0.697

AC:

2428

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.64

DANN

Benign

0.69

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