Variant rs10510911 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 0.387 in 151,988 control chromosomes in the GnomAD database, including 11,413 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 0.39 ( 11413 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0270

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=-1.01).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.397 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:

0.386

AC:

58689

AN:

151870

Hom.:

11391

Cov.:

show subpopulations

Gnomad AFR

AF:

0.370

Gnomad AMI

AF:

0.453

Gnomad AMR

AF:

0.405

Gnomad ASJ

AF:

0.343

Gnomad EAS

AF:

0.358

Gnomad SAS

AF:

0.292

Gnomad FIN

AF:

0.416

Gnomad MID

AF:

0.331

Gnomad NFE

AF:

0.398

Gnomad OTH

AF:

0.394

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

GnomAD4 genome

AF:

0.387

AC:

58762

AN:

151988

Hom.:

11413

Cov.:

AF XY:

0.385

AC XY:

28613

AN XY:

74292

show subpopulations

Gnomad4 AFR

AF:

0.370

Gnomad4 AMR

AF:

0.406

Gnomad4 ASJ

AF:

0.343

Gnomad4 EAS

AF:

0.359

Gnomad4 SAS

AF:

0.288

Gnomad4 FIN

AF:

0.416

Gnomad4 NFE

AF:

0.398

Gnomad4 OTH

AF:

0.396

Alfa

AF:

0.387

Hom.:

1609

Bravo

AF:

0.388

Asia WGS

AF:

0.351

AC:

1224

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

2.5

DANN

Benign

0.38

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