Variant 9-103582639-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 0.763 in 152,092 control chromosomes in the GnomAD database, including 44,499 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 0.76 ( 44499 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0570

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=-1.04).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.806 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:

0.762

AC:

115851

AN:

151974

Hom.:

44445

Cov.:

show subpopulations

Gnomad AFR

AF:

0.797

Gnomad AMI

AF:

0.770

Gnomad AMR

AF:

0.817

Gnomad ASJ

AF:

0.769

Gnomad EAS

AF:

0.816

Gnomad SAS

AF:

0.658

Gnomad FIN

AF:

0.796

Gnomad MID

AF:

0.712

Gnomad NFE

AF:

0.727

Gnomad OTH

AF:

0.756

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

GnomAD4 genome

AF:

0.763

AC:

115972

AN:

152092

Hom.:

44499

Cov.:

AF XY:

0.766

AC XY:

56960

AN XY:

74336

show subpopulations

Gnomad4 AFR

AF:

0.797

Gnomad4 AMR

AF:

0.818

Gnomad4 ASJ

AF:

0.769

Gnomad4 EAS

AF:

0.817

Gnomad4 SAS

AF:

0.658

Gnomad4 FIN

AF:

0.796

Gnomad4 NFE

AF:

0.727

Gnomad4 OTH

AF:

0.759

Alfa

AF:

0.738

Hom.:

22085

Bravo

AF:

0.772

Asia WGS

AF:

0.749

AC:

2605

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

7.2

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