X-140545365-T-C

Position:

• chrX-140545365-T-C

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 0.89 (31207 hom., 28551 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.302

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.140545365T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.892 AC: 97812 AN: 109635 Hom.: 31224 Cov.: 22 AF XY: 0.895 AC XY: 28517 AN XY: 31863

Gnomad AFR AF: 0.748

Gnomad AMI AF: 0.965

Gnomad AMR AF: 0.951

Gnomad ASJ AF: 0.962

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.952

Gnomad FIN AF: 0.954

Gnomad MID AF: 0.957

Gnomad NFE AF: 0.942

Gnomad OTH AF: 0.903

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: 0.892 AC: 97821 AN: 109688 Hom.: 31207 Cov.: 22 AF XY: 0.894 AC XY: 28551 AN XY: 31926

Gnomad4 AFR AF: 0.748

Gnomad4 AMR AF: 0.951

Gnomad4 ASJ AF: 0.962

Gnomad4 EAS AF: 0.987

Gnomad4 SAS AF: 0.950

Gnomad4 FIN AF: 0.954

Gnomad4 NFE AF: 0.942

Gnomad4 OTH AF: 0.899

Alfa AF: 0.930 Hom.: 75802

Bravo AF: 0.888

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.2
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs203652; hg19: chrX-139627530;