Variant rs10477360 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 0.437 in 151,870 control chromosomes in the GnomAD database, including 15,140 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 0.44 ( 15140 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0870

Variant links:

Genome browser will be placed here

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 = 0.544 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:

0.437

AC:

66305

AN:

151752

Hom.:

15138

Cov.:

show subpopulations

Gnomad AFR

AF:

0.304

Gnomad AMI

AF:

0.538

Gnomad AMR

AF:

0.553

Gnomad ASJ

AF:

0.449

Gnomad EAS

AF:

0.495

Gnomad SAS

AF:

0.508

Gnomad FIN

AF:

0.512

Gnomad MID

AF:

0.535

Gnomad NFE

AF:

0.467

Gnomad OTH

AF:

0.467

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

GnomAD4 genome

AF:

0.437

AC:

66315

AN:

151870

Hom.:

15140

Cov.:

AF XY:

0.442

AC XY:

32833

AN XY:

74216

show subpopulations

Gnomad4 AFR

AF:

0.303

Gnomad4 AMR

AF:

0.553

Gnomad4 ASJ

AF:

0.449

Gnomad4 EAS

AF:

0.494

Gnomad4 SAS

AF:

0.509

Gnomad4 FIN

AF:

0.512

Gnomad4 NFE

AF:

0.467

Gnomad4 OTH

AF:

0.467

Alfa

AF:

0.468

Hom.:

33821

Bravo

AF:

0.438

Asia WGS

AF:

0.520

AC:

1802

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

1.1

DANN

Benign

0.68

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