Variant rs10267337 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 0.905 in 152,164 control chromosomes in the GnomAD database, including 63,044 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 0.91 ( 63044 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.921

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=-0.97).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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:

0.906

AC:

137704

AN:

152046

Hom.:

63025

Cov.:

show subpopulations

Gnomad AFR

AF:

0.758

Gnomad AMI

AF:

0.895

Gnomad AMR

AF:

0.948

Gnomad ASJ

AF:

0.928

Gnomad EAS

AF:

1.00

Gnomad SAS

AF:

0.954

Gnomad FIN

AF:

0.973

Gnomad MID

AF:

0.889

Gnomad NFE

AF:

0.964

Gnomad OTH

AF:

0.907

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

GnomAD4 genome

AF:

0.905

AC:

137765

AN:

152164

Hom.:

63044

Cov.:

AF XY:

0.908

AC XY:

67597

AN XY:

74412

show subpopulations

Gnomad4 AFR

AF:

0.757

Gnomad4 AMR

AF:

0.948

Gnomad4 ASJ

AF:

0.928

Gnomad4 EAS

AF:

1.00

Gnomad4 SAS

AF:

0.954

Gnomad4 FIN

AF:

0.973

Gnomad4 NFE

AF:

0.964

Gnomad4 OTH

AF:

0.908

Alfa

AF:

0.935

Hom.:

27096

Bravo

AF:

0.896

Asia WGS

AF:

0.947

AC:

3290

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.40

DANN

Benign

0.69

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