Variant rs10908474 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 0.342 in 151,974 control chromosomes in the GnomAD database, including 9,268 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 0.34 ( 9268 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.12

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=-0.93).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.421 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:

0.342

AC:

51951

AN:

151856

Hom.:

9272

Cov.:

show subpopulations

Gnomad AFR

AF:

0.231

Gnomad AMI

AF:

0.425

Gnomad AMR

AF:

0.430

Gnomad ASJ

AF:

0.351

Gnomad EAS

AF:

0.327

Gnomad SAS

AF:

0.396

Gnomad FIN

AF:

0.378

Gnomad MID

AF:

0.385

Gnomad NFE

AF:

0.379

Gnomad OTH

AF:

0.367

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

GnomAD4 genome

AF:

0.342

AC:

51967

AN:

151974

Hom.:

9268

Cov.:

AF XY:

0.345

AC XY:

25588

AN XY:

74260

show subpopulations

Gnomad4 AFR

AF:

0.230

Gnomad4 AMR

AF:

0.430

Gnomad4 ASJ

AF:

0.351

Gnomad4 EAS

AF:

0.328

Gnomad4 SAS

AF:

0.397

Gnomad4 FIN

AF:

0.378

Gnomad4 NFE

AF:

0.379

Gnomad4 OTH

AF:

0.368

Alfa

AF:

0.373

Hom.:

8730

Bravo

AF:

0.345

Asia WGS

AF:

0.370

AC:

1286

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.015

DANN

Benign

0.37

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