Variant rs10734105 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 0.655 in 152,026 control chromosomes in the GnomAD database, including 33,190 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 0.66 ( 33190 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.435

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=-0.85).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.817 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:

0.655

AC:

99544

AN:

151908

Hom.:

33178

Cov.:

show subpopulations

Gnomad AFR

AF:

0.538

Gnomad AMI

AF:

0.756

Gnomad AMR

AF:

0.718

Gnomad ASJ

AF:

0.612

Gnomad EAS

AF:

0.838

Gnomad SAS

AF:

0.822

Gnomad FIN

AF:

0.609

Gnomad MID

AF:

0.659

Gnomad NFE

AF:

0.695

Gnomad OTH

AF:

0.643

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

GnomAD4 genome

AF:

0.655

AC:

99598

AN:

152026

Hom.:

33190

Cov.:

AF XY:

0.657

AC XY:

48789

AN XY:

74300

show subpopulations

Gnomad4 AFR

AF:

0.538

Gnomad4 AMR

AF:

0.718

Gnomad4 ASJ

AF:

0.612

Gnomad4 EAS

AF:

0.838

Gnomad4 SAS

AF:

0.820

Gnomad4 FIN

AF:

0.609

Gnomad4 NFE

AF:

0.695

Gnomad4 OTH

AF:

0.644

Alfa

AF:

0.683

Hom.:

39354

Bravo

AF:

0.653

Asia WGS

AF:

0.818

AC:

2841

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.78

DANN

Benign

0.39

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