Variant 10-103479506-T-C 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 0.722 in 157,344 control chromosomes in the GnomAD database, including 41,750 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 0.72 ( 40208 hom., cov: 33)

Exomes 𝑓: 0.76 ( 1542 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.570

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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.889 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:

0.720

AC:

109545

AN:

152080

Hom.:

40186

Cov.:

show subpopulations

Gnomad AFR

AF:

0.586

Gnomad AMI

AF:

0.675

Gnomad AMR

AF:

0.799

Gnomad ASJ

AF:

0.735

Gnomad EAS

AF:

0.910

Gnomad SAS

AF:

0.882

Gnomad FIN

AF:

0.795

Gnomad MID

AF:

0.734

Gnomad NFE

AF:

0.746

Gnomad OTH

AF:

0.729

GnomAD4 exome

AF:

0.763

AC:

3924

AN:

5146

Hom.:

1542

AF XY:

0.764

AC XY:

2037

AN XY:

2666

show subpopulations

Gnomad4 AFR exome

AF:

0.505

Gnomad4 AMR exome

AF:

0.808

Gnomad4 ASJ exome

AF:

0.746

Gnomad4 EAS exome

AF:

0.889

Gnomad4 SAS exome

AF:

0.877

Gnomad4 FIN exome

AF:

0.708

Gnomad4 NFE exome

AF:

0.741

Gnomad4 OTH exome

AF:

0.765

GnomAD4 genome

AF:

0.720

AC:

109614

AN:

152198

Hom.:

40208

Cov.:

AF XY:

0.728

AC XY:

54150

AN XY:

74412

show subpopulations

Gnomad4 AFR

AF:

0.586

Gnomad4 AMR

AF:

0.800

Gnomad4 ASJ

AF:

0.735

Gnomad4 EAS

AF:

0.910

Gnomad4 SAS

AF:

0.883

Gnomad4 FIN

AF:

0.795

Gnomad4 NFE

AF:

0.746

Gnomad4 OTH

AF:

0.731

Alfa

AF:

0.720

Hom.:

10011

Bravo

AF:

0.713

Asia WGS

AF:

0.891

AC:

3099

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

2.5

DANN

Benign

0.52

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