Variant rs11783752 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 0.697 in 152,080 control chromosomes in the GnomAD database, including 37,215 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 0.70 ( 37215 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.128

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=-0.87).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.758 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:

0.697

AC:

105960

AN:

151962

Hom.:

37190

Cov.:

show subpopulations

Gnomad AFR

AF:

0.712

Gnomad AMI

AF:

0.579

Gnomad AMR

AF:

0.769

Gnomad ASJ

AF:

0.780

Gnomad EAS

AF:

0.742

Gnomad SAS

AF:

0.652

Gnomad FIN

AF:

0.626

Gnomad MID

AF:

0.744

Gnomad NFE

AF:

0.679

Gnomad OTH

AF:

0.724

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

GnomAD4 genome

AF:

0.697

AC:

106043

AN:

152080

Hom.:

37215

Cov.:

AF XY:

0.696

AC XY:

51753

AN XY:

74326

show subpopulations

Gnomad4 AFR

AF:

0.712

Gnomad4 AMR

AF:

0.769

Gnomad4 ASJ

AF:

0.780

Gnomad4 EAS

AF:

0.743

Gnomad4 SAS

AF:

0.651

Gnomad4 FIN

AF:

0.626

Gnomad4 NFE

AF:

0.679

Gnomad4 OTH

AF:

0.727

Alfa

AF:

0.693

Hom.:

39570

Bravo

AF:

0.712

Asia WGS

AF:

0.712

AC:

2479

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.57

DANN

Benign

0.46

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