Variant rs10455025 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 0.242 in 152,146 control chromosomes in the GnomAD database, including 5,707 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 0.24 ( 5707 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.484

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=-0.86).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.34 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:

0.242

AC:

36740

AN:

152028

Hom.:

5706

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0750

Gnomad AMI

AF:

0.452

Gnomad AMR

AF:

0.278

Gnomad ASJ

AF:

0.369

Gnomad EAS

AF:

0.0408

Gnomad SAS

AF:

0.0898

Gnomad FIN

AF:

0.289

Gnomad MID

AF:

0.248

Gnomad NFE

AF:

0.344

Gnomad OTH

AF:

0.272

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

GnomAD4 genome

AF:

0.242

AC:

36747

AN:

152146

Hom.:

5707

Cov.:

AF XY:

0.234

AC XY:

17442

AN XY:

74388

show subpopulations

Gnomad4 AFR

AF:

0.0748

Gnomad4 AMR

AF:

0.278

Gnomad4 ASJ

AF:

0.369

Gnomad4 EAS

AF:

0.0407

Gnomad4 SAS

AF:

0.0911

Gnomad4 FIN

AF:

0.289

Gnomad4 NFE

AF:

0.344

Gnomad4 OTH

AF:

0.272

Alfa

AF:

0.320

Hom.:

7977

Bravo

AF:

0.241

Asia WGS

AF:

0.101

AC:

351

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.52

DANN

Benign

0.56

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