X-67120595-A-G

Position:

• chrX-67120595-A-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 0.65 (20379 hom., 21234 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.23

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

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: 0.652 AC: 71574 AN: 109793 Hom.: 20388 Cov.: 22 AF XY: 0.662 AC XY: 21219 AN XY: 32055

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.884

Gnomad AMR AF: 0.826

Gnomad ASJ AF: 0.919

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.919

Gnomad FIN AF: 0.828

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.843

Gnomad OTH AF: 0.700

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: 0.652 AC: 71566 AN: 109846 Hom.: 20379 Cov.: 22 AF XY: 0.661 AC XY: 21234 AN XY: 32118

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.827

Gnomad4 ASJ AF: 0.919

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.920

Gnomad4 FIN AF: 0.828

Gnomad4 NFE AF: 0.843

Gnomad4 OTH AF: 0.702

Alfa AF: 0.812 Hom.: 41402

Bravo AF: 0.635

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.5
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs925391; hg19: chrX-66340437;