Variant 10-117559349-G-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 0.502 in 152,094 control chromosomes in the GnomAD database, including 20,712 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 0.50 ( 20712 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.902

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=-0.99).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.605 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:

0.502

AC:

76267

AN:

151976

Hom.:

20707

Cov.:

show subpopulations

Gnomad AFR

AF:

0.292

Gnomad AMI

AF:

0.638

Gnomad AMR

AF:

0.562

Gnomad ASJ

AF:

0.543

Gnomad EAS

AF:

0.557

Gnomad SAS

AF:

0.410

Gnomad FIN

AF:

0.519

Gnomad MID

AF:

0.614

Gnomad NFE

AF:

0.610

Gnomad OTH

AF:

0.563

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

GnomAD4 genome

AF:

0.502

AC:

76302

AN:

152094

Hom.:

20712

Cov.:

AF XY:

0.497

AC XY:

36922

AN XY:

74334

show subpopulations

Gnomad4 AFR

AF:

0.292

Gnomad4 AMR

AF:

0.561

Gnomad4 ASJ

AF:

0.543

Gnomad4 EAS

AF:

0.557

Gnomad4 SAS

AF:

0.411

Gnomad4 FIN

AF:

0.519

Gnomad4 NFE

AF:

0.610

Gnomad4 OTH

AF:

0.566

Alfa

AF:

0.568

Hom.:

6392

Bravo

AF:

0.505

Asia WGS

AF:

0.428

AC:

1491

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.031

DANN

Benign

0.24

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