Variant rs10505975 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 0.795 in 152,146 control chromosomes in the GnomAD database, including 49,649 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 0.79 ( 49649 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.120

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=-0.82).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.89 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:

0.795

AC:

120845

AN:

152028

Hom.:

49629

Cov.:

show subpopulations

Gnomad AFR

AF:

0.564

Gnomad AMI

AF:

0.948

Gnomad AMR

AF:

0.828

Gnomad ASJ

AF:

0.875

Gnomad EAS

AF:

0.866

Gnomad SAS

AF:

0.823

Gnomad FIN

AF:

0.906

Gnomad MID

AF:

0.877

Gnomad NFE

AF:

0.896

Gnomad OTH

AF:

0.812

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

GnomAD4 genome

AF:

0.795

AC:

120914

AN:

152146

Hom.:

49649

Cov.:

AF XY:

0.796

AC XY:

59179

AN XY:

74388

show subpopulations

Gnomad4 AFR

AF:

0.564

Gnomad4 AMR

AF:

0.827

Gnomad4 ASJ

AF:

0.875

Gnomad4 EAS

AF:

0.866

Gnomad4 SAS

AF:

0.824

Gnomad4 FIN

AF:

0.906

Gnomad4 NFE

AF:

0.896

Gnomad4 OTH

AF:

0.809

Alfa

AF:

0.865

Hom.:

25138

Bravo

AF:

0.780

Asia WGS

AF:

0.792

AC:

2754

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

1.6

DANN

Benign

0.65

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