Variant 9-81383132-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 0.708 in 152,074 control chromosomes in the GnomAD database, including 38,961 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 0.71 ( 38961 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.387

Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.0).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.804 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:

0.708

AC:

107650

AN:

151956

Hom.:

38937

Cov.:

show subpopulations

Gnomad AFR

AF:

0.811

Gnomad AMI

AF:

0.737

Gnomad AMR

AF:

0.582

Gnomad ASJ

AF:

0.768

Gnomad EAS

AF:

0.360

Gnomad SAS

AF:

0.685

Gnomad FIN

AF:

0.682

Gnomad MID

AF:

0.650

Gnomad NFE

AF:

0.704

Gnomad OTH

AF:

0.684

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

GnomAD4 genome

AF:

0.708

AC:

107704

AN:

152074

Hom.:

38961

Cov.:

AF XY:

0.705

AC XY:

52435

AN XY:

74348

show subpopulations

Gnomad4 AFR

AF:

0.811

Gnomad4 AMR

AF:

0.581

Gnomad4 ASJ

AF:

0.768

Gnomad4 EAS

AF:

0.360

Gnomad4 SAS

AF:

0.684

Gnomad4 FIN

AF:

0.682

Gnomad4 NFE

AF:

0.704

Gnomad4 OTH

AF:

0.677

Alfa

AF:

0.697

Hom.:

48897

Bravo

AF:

0.701

Asia WGS

AF:

0.553

AC:

1926

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

2.1

DANN

Benign

0.44

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