Variant chrX-94590840-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

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 0.64 ( 16972 hom., 20179 hem., cov: 23)

Failed GnomAD Quality Control

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.799

Variant links:

Genes affected

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.97).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
	use as main transcript	n.94590840C>T	intergenic_region
LOC107985704	XR_001755914.2 linkuse as main transcript	n.219+9267G>A	intron_variant
LOC107985704	XR_001755915.2 linkuse as main transcript	n.219+9267G>A	intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.636

AC:

70105

AN:

110254

Hom.:

16980

Cov.:

AF XY:

0.620

AC XY:

20158

AN XY:

32514

show subpopulations

Gnomad AFR

AF:

0.599

Gnomad AMI

AF:

0.726

Gnomad AMR

AF:

0.424

Gnomad ASJ

AF:

0.811

Gnomad EAS

AF:

0.0170

Gnomad SAS

AF:

0.378

Gnomad FIN

AF:

0.760

Gnomad MID

AF:

0.668

Gnomad NFE

AF:

0.730

Gnomad OTH

AF:

0.626

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

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.636

AC:

70109

AN:

110310

Hom.:

16972

Cov.:

AF XY:

0.619

AC XY:

20179

AN XY:

32580

show subpopulations

Gnomad4 AFR

AF:

0.598

Gnomad4 AMR

AF:

0.424

Gnomad4 ASJ

AF:

0.811

Gnomad4 EAS

AF:

0.0171

Gnomad4 SAS

AF:

0.380

Gnomad4 FIN

AF:

0.760

Gnomad4 NFE

AF:

0.730

Gnomad4 OTH

AF:

0.618

Alfa

AF:

0.682

Hom.:

17735

Bravo

AF:

0.606

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

2.8

DANN

Benign

0.37

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