Variant rs10494580 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 0.605 in 152,050 control chromosomes in the GnomAD database, including 31,133 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 0.61 ( 31133 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.228

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=-0.91).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.749 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:

0.605

AC:

91992

AN:

151932

Hom.:

31134

Cov.:

show subpopulations

Gnomad AFR

AF:

0.268

Gnomad AMI

AF:

0.749

Gnomad AMR

AF:

0.725

Gnomad ASJ

AF:

0.724

Gnomad EAS

AF:

0.760

Gnomad SAS

AF:

0.769

Gnomad FIN

AF:

0.693

Gnomad MID

AF:

0.687

Gnomad NFE

AF:

0.736

Gnomad OTH

AF:

0.673

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

GnomAD4 genome

AF:

0.605

AC:

92016

AN:

152050

Hom.:

31133

Cov.:

AF XY:

0.610

AC XY:

45371

AN XY:

74324

show subpopulations

Gnomad4 AFR

AF:

0.268

Gnomad4 AMR

AF:

0.725

Gnomad4 ASJ

AF:

0.724

Gnomad4 EAS

AF:

0.760

Gnomad4 SAS

AF:

0.770

Gnomad4 FIN

AF:

0.693

Gnomad4 NFE

AF:

0.736

Gnomad4 OTH

AF:

0.672

Alfa

AF:

0.564

Hom.:

2054

Bravo

AF:

0.595

Asia WGS

AF:

0.709

AC:

2460

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.7

DANN

Benign

0.40

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