Variant chr10-99532698-C-A 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 0.537 in 152,010 control chromosomes in the GnomAD database, including 22,103 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 0.54 ( 22103 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.20

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=-0.77).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.607 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:

0.537

AC:

81531

AN:

151892

Hom.:

22071

Cov.:

show subpopulations

Gnomad AFR

AF:

0.563

Gnomad AMI

AF:

0.486

Gnomad AMR

AF:

0.571

Gnomad ASJ

AF:

0.459

Gnomad EAS

AF:

0.554

Gnomad SAS

AF:

0.626

Gnomad FIN

AF:

0.511

Gnomad MID

AF:

0.449

Gnomad NFE

AF:

0.516

Gnomad OTH

AF:

0.504

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

GnomAD4 genome

AF:

0.537

AC:

81611

AN:

152010

Hom.:

22103

Cov.:

AF XY:

0.539

AC XY:

40056

AN XY:

74304

show subpopulations

Gnomad4 AFR

AF:

0.563

Gnomad4 AMR

AF:

0.572

Gnomad4 ASJ

AF:

0.459

Gnomad4 EAS

AF:

0.554

Gnomad4 SAS

AF:

0.625

Gnomad4 FIN

AF:

0.511

Gnomad4 NFE

AF:

0.516

Gnomad4 OTH

AF:

0.500

Alfa

AF:

0.458

Hom.:

2114

Bravo

AF:

0.541

Asia WGS

AF:

0.600

AC:

2087

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

0.99

DANN

Benign

0.83

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