Variant rs10811469 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 0.118 in 151,850 control chromosomes in the GnomAD database, including 1,146 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 0.12 ( 1146 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.320

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 = 0.189 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:

0.118

AC:

17916

AN:

151732

Hom.:

1144

Cov.:

show subpopulations

Gnomad AFR

AF:

0.122

Gnomad AMI

AF:

0.103

Gnomad AMR

AF:

0.0830

Gnomad ASJ

AF:

0.199

Gnomad EAS

AF:

0.200

Gnomad SAS

AF:

0.166

Gnomad FIN

AF:

0.0540

Gnomad MID

AF:

0.247

Gnomad NFE

AF:

0.119

Gnomad OTH

AF:

0.128

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

GnomAD4 genome

AF:

0.118

AC:

17922

AN:

151850

Hom.:

1146

Cov.:

AF XY:

0.117

AC XY:

8653

AN XY:

74204

show subpopulations

Gnomad4 AFR

AF:

0.122

Gnomad4 AMR

AF:

0.0829

Gnomad4 ASJ

AF:

0.199

Gnomad4 EAS

AF:

0.199

Gnomad4 SAS

AF:

0.165

Gnomad4 FIN

AF:

0.0540

Gnomad4 NFE

AF:

0.119

Gnomad4 OTH

AF:

0.132

Alfa

AF:

0.0551

Hom.:

Bravo

AF:

0.121

Asia WGS

AF:

0.195

AC:

675

AN:

3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

3.8

DANN

Benign

0.74

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