Variant X-134229869-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 0.18 in 109,095 control chromosomes in the GnomAD database, including 1,717 homozygotes. There are 5,354 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 ( 1717 hom., 5354 hem., cov: 21)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.53

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=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.180

AC:

19643

AN:

109054

Hom.:

1717

Cov.:

AF XY:

0.169

AC XY:

5330

AN XY:

31490

show subpopulations

Gnomad AFR

AF:

0.264

Gnomad AMI

AF:

0.0618

Gnomad AMR

AF:

0.338

Gnomad ASJ

AF:

0.0720

Gnomad EAS

AF:

0.405

Gnomad SAS

AF:

0.292

Gnomad FIN

AF:

0.0807

Gnomad MID

AF:

0.0948

Gnomad NFE

AF:

0.101

Gnomad OTH

AF:

0.186

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

GnomAD4 genome

AF:

0.180

AC:

19668

AN:

109095

Hom.:

1717

Cov.:

AF XY:

0.170

AC XY:

5354

AN XY:

31541

show subpopulations

Gnomad4 AFR

AF:

0.264

Gnomad4 AMR

AF:

0.339

Gnomad4 ASJ

AF:

0.0720

Gnomad4 EAS

AF:

0.404

Gnomad4 SAS

AF:

0.292

Gnomad4 FIN

AF:

0.0807

Gnomad4 NFE

AF:

0.101

Gnomad4 OTH

AF:

0.187

Alfa

AF:

0.126

Hom.:

9489

Bravo

AF:

0.217

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

DANN

Benign

0.76

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