Variant rs10175798 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 0.513 in 151,944 control chromosomes in the GnomAD database, including 21,298 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 0.51 ( 21298 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=-0.48).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.608 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:

0.513

AC:

77851

AN:

151826

Hom.:

21290

Cov.:

show subpopulations

Gnomad AFR

AF:

0.315

Gnomad AMI

AF:

0.577

Gnomad AMR

AF:

0.594

Gnomad ASJ

AF:

0.627

Gnomad EAS

AF:

0.354

Gnomad SAS

AF:

0.472

Gnomad FIN

AF:

0.573

Gnomad MID

AF:

0.604

Gnomad NFE

AF:

0.613

Gnomad OTH

AF:

0.531

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

GnomAD4 genome

AF:

0.513

AC:

77889

AN:

151944

Hom.:

21298

Cov.:

AF XY:

0.511

AC XY:

37951

AN XY:

74242

show subpopulations

Gnomad4 AFR

AF:

0.315

Gnomad4 AMR

AF:

0.593

Gnomad4 ASJ

AF:

0.627

Gnomad4 EAS

AF:

0.355

Gnomad4 SAS

AF:

0.473

Gnomad4 FIN

AF:

0.573

Gnomad4 NFE

AF:

0.613

Gnomad4 OTH

AF:

0.533

Alfa

AF:

0.508

Hom.:

3071

Bravo

AF:

0.508

Asia WGS

AF:

0.404

AC:

1408

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.48

CADD

Benign

DANN

Benign

0.81

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