Variant rs1335159 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 0.953 in 151,870 control chromosomes in the GnomAD database, including 69,094 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 0.95 ( 69094 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.12

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=-0.91).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.953

AC:

144591

AN:

151752

Hom.:

69045

Cov.:

show subpopulations

Gnomad AFR

AF:

0.878

Gnomad AMI

AF:

0.997

Gnomad AMR

AF:

0.975

Gnomad ASJ

AF:

0.978

Gnomad EAS

AF:

0.952

Gnomad SAS

AF:

0.969

Gnomad FIN

AF:

0.999

Gnomad MID

AF:

0.968

Gnomad NFE

AF:

0.983

Gnomad OTH

AF:

0.956

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

GnomAD4 genome

AF:

0.953

AC:

144696

AN:

151870

Hom.:

69094

Cov.:

AF XY:

0.954

AC XY:

70814

AN XY:

74234

show subpopulations

Gnomad4 AFR

AF:

0.878

Gnomad4 AMR

AF:

0.975

Gnomad4 ASJ

AF:

0.978

Gnomad4 EAS

AF:

0.952

Gnomad4 SAS

AF:

0.969

Gnomad4 FIN

AF:

0.999

Gnomad4 NFE

AF:

0.983

Gnomad4 OTH

AF:

0.956

Alfa

AF:

0.971

Hom.:

11703

Bravo

AF:

0.948

Asia WGS

AF:

0.952

AC:

3300

AN:

3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.70

DANN

Benign

0.23

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