Variant chr10-88106892-C-T 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 0.249 in 152,086 control chromosomes in the GnomAD database, including 5,117 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 0.25 ( 5117 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.21

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 (EAS) allele frequency at 95% confidence interval = 0.453 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:

0.250

AC:

37945

AN:

151968

Hom.:

5119

Cov.:

show subpopulations

Gnomad AFR

AF:

0.179

Gnomad AMI

AF:

0.239

Gnomad AMR

AF:

0.197

Gnomad ASJ

AF:

0.252

Gnomad EAS

AF:

0.469

Gnomad SAS

AF:

0.318

Gnomad FIN

AF:

0.279

Gnomad MID

AF:

0.225

Gnomad NFE

AF:

0.279

Gnomad OTH

AF:

0.244

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

GnomAD4 genome

AF:

0.249

AC:

37943

AN:

152086

Hom.:

5117

Cov.:

AF XY:

0.252

AC XY:

18735

AN XY:

74336

show subpopulations

Gnomad4 AFR

AF:

0.179

Gnomad4 AMR

AF:

0.197

Gnomad4 ASJ

AF:

0.252

Gnomad4 EAS

AF:

0.469

Gnomad4 SAS

AF:

0.319

Gnomad4 FIN

AF:

0.279

Gnomad4 NFE

AF:

0.279

Gnomad4 OTH

AF:

0.243

Alfa

AF:

0.272

Hom.:

11888

Bravo

AF:

0.239

Asia WGS

AF:

0.349

AC:

1217

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

0.66

DANN

Benign

0.42

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