Variant chrX-141136709-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 0.52 ( 10694 hom., 14895 hem., cov: 20)

Failed GnomAD Quality Control

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.75

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=-0.93).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.141136709C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LDOC1	ENST00000670989.1 linkuse as main transcript	n.207-17137G>A		intron_variant

Frequencies

GnomAD3 genomes

AF:

0.517

AC:

54421

AN:

105186

Hom.:

10692

Cov.:

AF XY:

0.528

AC XY:

14890

AN XY:

28196

show subpopulations

Gnomad AFR

AF:

0.355

Gnomad AMI

AF:

0.309

Gnomad AMR

AF:

0.478

Gnomad ASJ

AF:

0.546

Gnomad EAS

AF:

0.408

Gnomad SAS

AF:

0.568

Gnomad FIN

AF:

0.640

Gnomad MID

AF:

0.581

Gnomad NFE

AF:

0.612

Gnomad OTH

AF:

0.518

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:

0.517

AC:

54422

AN:

105208

Hom.:

10694

Cov.:

AF XY:

0.528

AC XY:

14895

AN XY:

28228

show subpopulations

Gnomad4 AFR

AF:

0.355

Gnomad4 AMR

AF:

0.478

Gnomad4 ASJ

AF:

0.546

Gnomad4 EAS

AF:

0.407

Gnomad4 SAS

AF:

0.568

Gnomad4 FIN

AF:

0.640

Gnomad4 NFE

AF:

0.612

Gnomad4 OTH

AF:

0.521

Alfa

AF:

0.583

Hom.:

39383

Bravo

AF:

0.490

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.024

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