Variant rs11717333 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 0.44 in 152,064 control chromosomes in the GnomAD database, including 15,020 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 0.44 ( 15020 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.479

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=-0.95).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.539 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:

0.440

AC:

66907

AN:

151946

Hom.:

15016

Cov.:

show subpopulations

Gnomad AFR

AF:

0.498

Gnomad AMI

AF:

0.313

Gnomad AMR

AF:

0.326

Gnomad ASJ

AF:

0.410

Gnomad EAS

AF:

0.556

Gnomad SAS

AF:

0.540

Gnomad FIN

AF:

0.505

Gnomad MID

AF:

0.383

Gnomad NFE

AF:

0.410

Gnomad OTH

AF:

0.410

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

GnomAD4 genome

AF:

0.440

AC:

66952

AN:

152064

Hom.:

15020

Cov.:

AF XY:

0.446

AC XY:

33119

AN XY:

74320

show subpopulations

Gnomad4 AFR

AF:

0.497

Gnomad4 AMR

AF:

0.326

Gnomad4 ASJ

AF:

0.410

Gnomad4 EAS

AF:

0.556

Gnomad4 SAS

AF:

0.540

Gnomad4 FIN

AF:

0.505

Gnomad4 NFE

AF:

0.410

Gnomad4 OTH

AF:

0.414

Alfa

AF:

0.420

Hom.:

7252

Bravo

AF:

0.426

Asia WGS

AF:

0.569

AC:

1976

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

1.4

DANN

Benign

0.82

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