Variant rs156243 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 0.657 in 151,444 control chromosomes in the GnomAD database, including 37,479 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 0.66 ( 37479 hom., cov: 28)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.831

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=-0.89).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.829 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:

0.657

AC:

99442

AN:

151326

Hom.:

37478

Cov.:

show subpopulations

Gnomad AFR

AF:

0.253

Gnomad AMI

AF:

0.747

Gnomad AMR

AF:

0.758

Gnomad ASJ

AF:

0.765

Gnomad EAS

AF:

0.706

Gnomad SAS

AF:

0.785

Gnomad FIN

AF:

0.812

Gnomad MID

AF:

0.696

Gnomad NFE

AF:

0.835

Gnomad OTH

AF:

0.681

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

GnomAD4 genome

AF:

0.657

AC:

99460

AN:

151444

Hom.:

37479

Cov.:

AF XY:

0.658

AC XY:

48702

AN XY:

73980

show subpopulations

Gnomad4 AFR

AF:

0.253

Gnomad4 AMR

AF:

0.758

Gnomad4 ASJ

AF:

0.765

Gnomad4 EAS

AF:

0.707

Gnomad4 SAS

AF:

0.785

Gnomad4 FIN

AF:

0.812

Gnomad4 NFE

AF:

0.835

Gnomad4 OTH

AF:

0.683

Alfa

AF:

0.770

Hom.:

10300

Bravo

AF:

0.633

Asia WGS

AF:

0.723

AC:

2511

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

DANN

Benign

0.54

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