Variant rs10465428 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 0.422 in 108,561 control chromosomes in the GnomAD database, including 7,691 homozygotes. There are 13,536 hemizygotes in GnomAD. 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 0.42 ( 7691 hom., 13536 hem., cov: 21)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.16

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=-0.96).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.968 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:

0.423

AC:

45849

AN:

108506

Hom.:

7693

Cov.:

AF XY:

0.437

AC XY:

13512

AN XY:

30924

show subpopulations

Gnomad AFR

AF:

0.268

Gnomad AMI

AF:

0.275

Gnomad AMR

AF:

0.614

Gnomad ASJ

AF:

0.479

Gnomad EAS

AF:

0.997

Gnomad SAS

AF:

0.760

Gnomad FIN

AF:

0.446

Gnomad MID

AF:

0.472

Gnomad NFE

AF:

0.416

Gnomad OTH

AF:

0.449

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

GnomAD4 genome

AF:

0.422

AC:

45866

AN:

108561

Hom.:

7691

Cov.:

AF XY:

0.437

AC XY:

13536

AN XY:

30989

show subpopulations

Gnomad4 AFR

AF:

0.268

Gnomad4 AMR

AF:

0.614

Gnomad4 ASJ

AF:

0.479

Gnomad4 EAS

AF:

0.996

Gnomad4 SAS

AF:

0.759

Gnomad4 FIN

AF:

0.446

Gnomad4 NFE

AF:

0.416

Gnomad4 OTH

AF:

0.458

Alfa

AF:

0.249

Hom.:

1171

Bravo

AF:

0.435

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.65

DANN

Benign

0.80

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