Variant rs11846868 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 0.586 in 152,104 control chromosomes in the GnomAD database, including 27,141 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 0.59 ( 27141 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.138

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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.964 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:

0.586

AC:

89114

AN:

151986

Hom.:

27129

Cov.:

show subpopulations

Gnomad AFR

AF:

0.675

Gnomad AMI

AF:

0.453

Gnomad AMR

AF:

0.435

Gnomad ASJ

AF:

0.587

Gnomad EAS

AF:

0.987

Gnomad SAS

AF:

0.779

Gnomad FIN

AF:

0.510

Gnomad MID

AF:

0.633

Gnomad NFE

AF:

0.536

Gnomad OTH

AF:

0.577

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

GnomAD4 genome

AF:

0.586

AC:

89163

AN:

152104

Hom.:

27141

Cov.:

AF XY:

0.588

AC XY:

43733

AN XY:

74346

show subpopulations

Gnomad4 AFR

AF:

0.675

Gnomad4 AMR

AF:

0.435

Gnomad4 ASJ

AF:

0.587

Gnomad4 EAS

AF:

0.987

Gnomad4 SAS

AF:

0.778

Gnomad4 FIN

AF:

0.510

Gnomad4 NFE

AF:

0.536

Gnomad4 OTH

AF:

0.579

Alfa

AF:

0.544

Hom.:

3931

Bravo

AF:

0.581

Asia WGS

AF:

0.829

AC:

2883

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

2.6

DANN

Benign

0.76

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