Variant rs10125157 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 0.0871 in 152,024 control chromosomes in the GnomAD database, including 806 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 0.087 ( 806 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.501

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=-0.96).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.253 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:

0.0871

AC:

13230

AN:

151906

Hom.:

808

Cov.:

show subpopulations

Gnomad AFR

AF:

0.132

Gnomad AMI

AF:

0.0274

Gnomad AMR

AF:

0.0752

Gnomad ASJ

AF:

0.0876

Gnomad EAS

AF:

0.212

Gnomad SAS

AF:

0.265

Gnomad FIN

AF:

0.0677

Gnomad MID

AF:

0.171

Gnomad NFE

AF:

0.0439

Gnomad OTH

AF:

0.0896

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

GnomAD4 genome

AF:

0.0871

AC:

13236

AN:

152024

Hom.:

806

Cov.:

AF XY:

0.0924

AC XY:

6870

AN XY:

74314

show subpopulations

Gnomad4 AFR

AF:

0.131

Gnomad4 AMR

AF:

0.0748

Gnomad4 ASJ

AF:

0.0876

Gnomad4 EAS

AF:

0.211

Gnomad4 SAS

AF:

0.265

Gnomad4 FIN

AF:

0.0677

Gnomad4 NFE

AF:

0.0439

Gnomad4 OTH

AF:

0.0944

Alfa

AF:

0.0448

Hom.:

Bravo

AF:

0.0879

Asia WGS

AF:

0.218

AC:

756

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

3.6

DANN

Benign

0.66

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