Variant chr10-53600475-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 0.677 in 152,120 control chromosomes in the GnomAD database, including 35,849 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 0.68 ( 35849 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.00

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=-1.02).

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:

0.677

AC:

102966

AN:

152002

Hom.:

35818

Cov.:

show subpopulations

Gnomad AFR

AF:

0.792

Gnomad AMI

AF:

0.640

Gnomad AMR

AF:

0.664

Gnomad ASJ

AF:

0.563

Gnomad EAS

AF:

0.991

Gnomad SAS

AF:

0.807

Gnomad FIN

AF:

0.569

Gnomad MID

AF:

0.703

Gnomad NFE

AF:

0.600

Gnomad OTH

AF:

0.681

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

GnomAD4 genome

AF:

0.677

AC:

103048

AN:

152120

Hom.:

35849

Cov.:

AF XY:

0.680

AC XY:

50604

AN XY:

74374

show subpopulations

Gnomad4 AFR

AF:

0.792

Gnomad4 AMR

AF:

0.664

Gnomad4 ASJ

AF:

0.563

Gnomad4 EAS

AF:

0.991

Gnomad4 SAS

AF:

0.806

Gnomad4 FIN

AF:

0.569

Gnomad4 NFE

AF:

0.600

Gnomad4 OTH

AF:

0.685

Alfa

AF:

0.528

Hom.:

1591

Bravo

AF:

0.686

Asia WGS

AF:

0.878

AC:

3050

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.45

DANN

Benign

0.40

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