X-138206413-A-T

Position:

• chrX-138206413-A-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 0.72 (20340 hom., 22906 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.350

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.138206413A>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.715 AC: 78556 AN: 109820 Hom.: 20344 Cov.: 23 AF XY: 0.711 AC XY: 22858 AN XY: 32128

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.777

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.675

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.860

Gnomad FIN AF: 0.799

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.789

Gnomad OTH AF: 0.692

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: 0.715 AC: 78593 AN: 109872 Hom.: 20340 Cov.: 23 AF XY: 0.712 AC XY: 22906 AN XY: 32190

Gnomad4 AFR AF: 0.615

Gnomad4 AMR AF: 0.636

Gnomad4 ASJ AF: 0.675

Gnomad4 EAS AF: 0.489

Gnomad4 SAS AF: 0.860

Gnomad4 FIN AF: 0.799

Gnomad4 NFE AF: 0.789

Gnomad4 OTH AF: 0.693

Alfa AF: 0.754 Hom.: 6217

Bravo AF: 0.693

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.1
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs398262; hg19: chrX-137288572;