Variant X-134287375-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 0.176 in 111,203 control chromosomes in the GnomAD database, including 1,533 homozygotes. There are 5,959 hemizygotes in GnomAD. 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 0.18 ( 1533 hom., 5959 hem., cov: 22)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.45

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=-1.01).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.396 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:

0.176

AC:

19553

AN:

111152

Hom.:

1531

Cov.:

AF XY:

0.177

AC XY:

5929

AN XY:

33422

show subpopulations

Gnomad AFR

AF:

0.228

Gnomad AMI

AF:

0.0644

Gnomad AMR

AF:

0.348

Gnomad ASJ

AF:

0.0886

Gnomad EAS

AF:

0.414

Gnomad SAS

AF:

0.304

Gnomad FIN

AF:

0.0979

Gnomad MID

AF:

0.0970

Gnomad NFE

AF:

0.105

Gnomad OTH

AF:

0.178

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

GnomAD4 genome

AF:

0.176

AC:

19587

AN:

111203

Hom.:

1533

Cov.:

AF XY:

0.178

AC XY:

5959

AN XY:

33483

show subpopulations

Gnomad4 AFR

AF:

0.228

Gnomad4 AMR

AF:

0.349

Gnomad4 ASJ

AF:

0.0886

Gnomad4 EAS

AF:

0.414

Gnomad4 SAS

AF:

0.303

Gnomad4 FIN

AF:

0.0979

Gnomad4 NFE

AF:

0.105

Gnomad4 OTH

AF:

0.179

Alfa

AF:

0.138

Hom.:

2371

Bravo

AF:

0.202

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.87

DANN

Benign

0.57

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