Variant rs10500664 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 0.849 in 152,040 control chromosomes in the GnomAD database, including 55,694 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 0.85 ( 55694 hom., cov: 30)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.180

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 (EAS) allele frequency at 95% confidence interval = 0.964 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:

0.849

AC:

129046

AN:

151924

Hom.:

55652

Cov.:

show subpopulations

Gnomad AFR

AF:

0.686

Gnomad AMI

AF:

0.936

Gnomad AMR

AF:

0.909

Gnomad ASJ

AF:

0.913

Gnomad EAS

AF:

0.987

Gnomad SAS

AF:

0.781

Gnomad FIN

AF:

0.949

Gnomad MID

AF:

0.896

Gnomad NFE

AF:

0.908

Gnomad OTH

AF:

0.871

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

GnomAD4 genome

AF:

0.849

AC:

129145

AN:

152040

Hom.:

55694

Cov.:

AF XY:

0.852

AC XY:

63329

AN XY:

74344

show subpopulations

Gnomad4 AFR

AF:

0.687

Gnomad4 AMR

AF:

0.909

Gnomad4 ASJ

AF:

0.913

Gnomad4 EAS

AF:

0.987

Gnomad4 SAS

AF:

0.781

Gnomad4 FIN

AF:

0.949

Gnomad4 NFE

AF:

0.908

Gnomad4 OTH

AF:

0.872

Alfa

AF:

0.886

Hom.:

28094

Bravo

AF:

0.841

Asia WGS

AF:

0.847

AC:

2946

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

4.5

DANN

Benign

0.57

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