Variant rs1150226 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 0.892 in 287,354 control chromosomes in the GnomAD database, including 115,756 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 0.86 ( 57429 hom., cov: 29)

Exomes 𝑓: 0.93 ( 58327 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.52

Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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:

0.862

AC:

130861

AN:

151792

Hom.:

57406

Cov.:

show subpopulations

Gnomad AFR

AF:

0.682

Gnomad AMI

AF:

0.879

Gnomad AMR

AF:

0.913

Gnomad ASJ

AF:

0.969

Gnomad EAS

AF:

0.999

Gnomad SAS

AF:

0.958

Gnomad FIN

AF:

0.967

Gnomad MID

AF:

0.889

Gnomad NFE

AF:

0.920

Gnomad OTH

AF:

0.877

GnomAD4 exome

AF:

0.926

AC:

125441

AN:

135448

Hom.:

58327

AF XY:

0.929

AC XY:

66235

AN XY:

71298

show subpopulations

Gnomad4 AFR exome

AF:

0.663

Gnomad4 AMR exome

AF:

0.926

Gnomad4 ASJ exome

AF:

0.972

Gnomad4 EAS exome

AF:

1.00

Gnomad4 SAS exome

AF:

0.955

Gnomad4 FIN exome

AF:

0.966

Gnomad4 NFE exome

AF:

0.922

Gnomad4 OTH exome

AF:

0.924

GnomAD4 genome

AF:

0.862

AC:

130935

AN:

151906

Hom.:

57429

Cov.:

AF XY:

0.867

AC XY:

64371

AN XY:

74230

show subpopulations

Gnomad4 AFR

AF:

0.681

Gnomad4 AMR

AF:

0.914

Gnomad4 ASJ

AF:

0.969

Gnomad4 EAS

AF:

0.999

Gnomad4 SAS

AF:

0.958

Gnomad4 FIN

AF:

0.967

Gnomad4 NFE

AF:

0.920

Gnomad4 OTH

AF:

0.878

Alfa

AF:

0.906

Hom.:

84713

Bravo

AF:

0.850

Asia WGS

AF:

0.964

AC:

3354

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.48

DANN

Benign

0.72

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