rs7056485

Positions:

• chrX-142079179-C-T

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 0.56 (13449 hom., 17436 hem., cov: 21)
  • Failed GnomAD Quality Control
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0720

Genes affected

(HGNC:):

ACMG classification

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	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.142079179C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000288098	ENST00000664519.1	n.223-116528C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.560 AC: 60916 AN: 108866 Hom.: 13448 Cov.: 21 AF XY: 0.557 AC XY: 17385 AN XY: 31220

Gnomad AFR AF: 0.788

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.601

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: 0.560 AC: 60968 AN: 108916 Hom.: 13449 Cov.: 21 AF XY: 0.557 AC XY: 17436 AN XY: 31280

Gnomad4 AFR AF: 0.788

Gnomad4 AMR AF: 0.684

Gnomad4 ASJ AF: 0.531

Gnomad4 EAS AF: 0.651

Gnomad4 SAS AF: 0.520

Gnomad4 FIN AF: 0.467

Gnomad4 NFE AF: 0.417

Gnomad4 OTH AF: 0.602

Alfa AF: 0.457 Hom.: 36527

Bravo AF: 0.596

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.7
DANN	Benign	0.42

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7056485; hg19: chrX-141166965;