Variant rs10496611 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 0.297 in 151,866 control chromosomes in the GnomAD database, including 7,193 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 0.30 ( 7193 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.118

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 (EAS) allele frequency at 95% confidence interval = 0.404 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:

0.298

AC:

45153

AN:

151748

Hom.:

7190

Cov.:

show subpopulations

Gnomad AFR

AF:

0.210

Gnomad AMI

AF:

0.393

Gnomad AMR

AF:

0.231

Gnomad ASJ

AF:

0.310

Gnomad EAS

AF:

0.420

Gnomad SAS

AF:

0.372

Gnomad FIN

AF:

0.425

Gnomad MID

AF:

0.328

Gnomad NFE

AF:

0.329

Gnomad OTH

AF:

0.296

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

GnomAD4 genome

AF:

0.297

AC:

45155

AN:

151866

Hom.:

7193

Cov.:

AF XY:

0.302

AC XY:

22414

AN XY:

74208

show subpopulations

Gnomad4 AFR

AF:

0.210

Gnomad4 AMR

AF:

0.230

Gnomad4 ASJ

AF:

0.310

Gnomad4 EAS

AF:

0.419

Gnomad4 SAS

AF:

0.373

Gnomad4 FIN

AF:

0.425

Gnomad4 NFE

AF:

0.329

Gnomad4 OTH

AF:

0.294

Alfa

AF:

0.300

Hom.:

3972

Bravo

AF:

0.278

Asia WGS

AF:

0.350

AC:

1217

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

1.2

DANN

Benign

0.85

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