X-51544937-T-G

Position:

• chrX-51544937-T-G

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 0.66 (17028 hom., 20914 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.112

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.656 AC: 72014 AN: 109757 Hom.: 17030 Cov.: 22 AF XY: 0.652 AC XY: 20888 AN XY: 32025

Gnomad AFR AF: 0.632

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.777

Gnomad ASJ AF: 0.749

Gnomad EAS AF: 0.925

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.678

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.670

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: 0.656 AC: 72032 AN: 109812 Hom.: 17028 Cov.: 22 AF XY: 0.652 AC XY: 20914 AN XY: 32090

Gnomad4 AFR AF: 0.632

Gnomad4 AMR AF: 0.778

Gnomad4 ASJ AF: 0.749

Gnomad4 EAS AF: 0.925

Gnomad4 SAS AF: 0.714

Gnomad4 FIN AF: 0.554

Gnomad4 NFE AF: 0.633

Gnomad4 OTH AF: 0.674

Alfa AF: 0.648 Hom.: 10835

Bravo AF: 0.677

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.2
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: rs1541241; hg19: chrX-51287789;