Variant rs889312 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The variant allele was found at a frequency of 0.682 in 151,942 control chromosomes in the GnomAD database, including 35,558 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 0.68 ( 35558 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.23

Variant links:

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ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.43).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.712 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:

0.682

AC:

103504

AN:

151824

Hom.:

35543

Cov.:

show subpopulations

Gnomad AFR

AF:

0.666

Gnomad AMI

AF:

0.672

Gnomad AMR

AF:

0.611

Gnomad ASJ

AF:

0.682

Gnomad EAS

AF:

0.450

Gnomad SAS

AF:

0.612

Gnomad FIN

AF:

0.767

Gnomad MID

AF:

0.671

Gnomad NFE

AF:

0.717

Gnomad OTH

AF:

0.673

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

GnomAD4 genome

AF:

0.682

AC:

103549

AN:

151942

Hom.:

35558

Cov.:

AF XY:

0.678

AC XY:

50338

AN XY:

74262

show subpopulations

Gnomad4 AFR

AF:

0.665

Gnomad4 AMR

AF:

0.610

Gnomad4 ASJ

AF:

0.682

Gnomad4 EAS

AF:

0.450

Gnomad4 SAS

AF:

0.612

Gnomad4 FIN

AF:

0.767

Gnomad4 NFE

AF:

0.717

Gnomad4 OTH

AF:

0.669

Alfa

AF:

0.698

Hom.:

76889

Bravo

AF:

0.668

Asia WGS

AF:

0.548

AC:

1904

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.43

CADD

Benign

DANN

Benign

0.79

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