Variant rs10490649 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 0.182 in 151,858 control chromosomes in the GnomAD database, including 2,815 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 0.18 ( 2815 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.137

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=-0.89).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.225 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:

0.182

AC:

27677

AN:

151740

Hom.:

2813

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0883

Gnomad AMI

AF:

0.249

Gnomad AMR

AF:

0.232

Gnomad ASJ

AF:

0.186

Gnomad EAS

AF:

0.224

Gnomad SAS

AF:

0.201

Gnomad FIN

AF:

0.207

Gnomad MID

AF:

0.114

Gnomad NFE

AF:

0.220

Gnomad OTH

AF:

0.180

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

GnomAD4 genome

AF:

0.182

AC:

27698

AN:

151858

Hom.:

2815

Cov.:

AF XY:

0.183

AC XY:

13592

AN XY:

74202

show subpopulations

Gnomad4 AFR

AF:

0.0882

Gnomad4 AMR

AF:

0.231

Gnomad4 ASJ

AF:

0.186

Gnomad4 EAS

AF:

0.224

Gnomad4 SAS

AF:

0.202

Gnomad4 FIN

AF:

0.207

Gnomad4 NFE

AF:

0.220

Gnomad4 OTH

AF:

0.183

Alfa

AF:

0.204

Hom.:

425

Bravo

AF:

0.180

Asia WGS

AF:

0.251

AC:

870

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

6.3

DANN

Benign

0.80

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