Variant rs1159918 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 0.536 in 151,934 control chromosomes in the GnomAD database, including 23,924 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 0.54 ( 23924 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.122

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=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.803 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:

0.536

AC:

81439

AN:

151816

Hom.:

23930

Cov.:

show subpopulations

Gnomad AFR

AF:

0.301

Gnomad AMI

AF:

0.806

Gnomad AMR

AF:

0.461

Gnomad ASJ

AF:

0.691

Gnomad EAS

AF:

0.823

Gnomad SAS

AF:

0.633

Gnomad FIN

AF:

0.553

Gnomad MID

AF:

0.655

Gnomad NFE

AF:

0.652

Gnomad OTH

AF:

0.575

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

GnomAD4 genome

AF:

0.536

AC:

81443

AN:

151934

Hom.:

23924

Cov.:

AF XY:

0.532

AC XY:

39529

AN XY:

74258

show subpopulations

Gnomad4 AFR

AF:

0.301

Gnomad4 AMR

AF:

0.460

Gnomad4 ASJ

AF:

0.691

Gnomad4 EAS

AF:

0.823

Gnomad4 SAS

AF:

0.633

Gnomad4 FIN

AF:

0.553

Gnomad4 NFE

AF:

0.652

Gnomad4 OTH

AF:

0.571

Alfa

AF:

0.628

Hom.:

41064

Bravo

AF:

0.516

Asia WGS

AF:

0.582

AC:

2024

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.4

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