Variant rs11007349 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 0.0942 in 152,116 control chromosomes in the GnomAD database, including 1,061 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 0.094 ( 1061 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.280

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=-0.83).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.386 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:

0.0941

AC:

14306

AN:

151998

Hom.:

1053

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0912

Gnomad AMI

AF:

0.205

Gnomad AMR

AF:

0.0977

Gnomad ASJ

AF:

0.0865

Gnomad EAS

AF:

0.400

Gnomad SAS

AF:

0.191

Gnomad FIN

AF:

0.0696

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.0680

Gnomad OTH

AF:

0.0885

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

GnomAD4 genome

AF:

0.0942

AC:

14333

AN:

152116

Hom.:

1061

Cov.:

AF XY:

0.0971

AC XY:

7216

AN XY:

74344

show subpopulations

Gnomad4 AFR

AF:

0.0913

Gnomad4 AMR

AF:

0.0975

Gnomad4 ASJ

AF:

0.0865

Gnomad4 EAS

AF:

0.401

Gnomad4 SAS

AF:

0.190

Gnomad4 FIN

AF:

0.0696

Gnomad4 NFE

AF:

0.0680

Gnomad4 OTH

AF:

0.0985

Alfa

AF:

0.0804

Hom.:

Bravo

AF:

0.0959

Asia WGS

AF:

0.292

AC:

1015

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

DANN

Benign

0.89

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