Variant rs11976165 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 0.218 in 152,082 control chromosomes in the GnomAD database, including 3,784 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 0.22 ( 3784 hom., cov: 33)

Failed GnomAD Quality Control

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.837

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=-0.82).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.272 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:

0.218

AC:

33128

AN:

151964

Hom.:

3772

Cov.:

show subpopulations

Gnomad AFR

AF:

0.277

Gnomad AMI

AF:

0.251

Gnomad AMR

AF:

0.245

Gnomad ASJ

AF:

0.183

Gnomad EAS

AF:

0.0908

Gnomad SAS

AF:

0.203

Gnomad FIN

AF:

0.169

Gnomad MID

AF:

0.184

Gnomad NFE

AF:

0.197

Gnomad OTH

AF:

0.204

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

GnomAD4 genome

AF:

0.218

AC:

33164

AN:

152082

Hom.:

3784

Cov.:

AF XY:

0.217

AC XY:

16165

AN XY:

74346

show subpopulations

Gnomad4 AFR

AF:

0.276

Gnomad4 AMR

AF:

0.245

Gnomad4 ASJ

AF:

0.183

Gnomad4 EAS

AF:

0.0907

Gnomad4 SAS

AF:

0.204

Gnomad4 FIN

AF:

0.169

Gnomad4 NFE

AF:

0.197

Gnomad4 OTH

AF:

0.200

Alfa

AF:

0.213

Hom.:

600

Bravo

AF:

0.227

Asia WGS

AF:

0.174

AC:

604

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

5.0

DANN

Benign

0.33

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