X-103324188-A-C

Position:

• chrX-103324188-A-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 0.67 (18715 hom., 21519 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.175

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).

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: 0.671 AC: 73953 AN: 110211 Hom.: 18712 Cov.: 23 AF XY: 0.661 AC XY: 21458 AN XY: 32453

Gnomad AFR AF: 0.911

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.669

Gnomad EAS AF: 0.599

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.543

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.642

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: 0.671 AC: 74006 AN: 110264 Hom.: 18715 Cov.: 23 AF XY: 0.662 AC XY: 21519 AN XY: 32516

Gnomad4 AFR AF: 0.911

Gnomad4 AMR AF: 0.619

Gnomad4 ASJ AF: 0.669

Gnomad4 EAS AF: 0.599

Gnomad4 SAS AF: 0.742

Gnomad4 FIN AF: 0.470

Gnomad4 NFE AF: 0.572

Gnomad4 OTH AF: 0.642

Alfa AF: 0.617 Hom.: 4846

Bravo AF: 0.691

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.6
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5987724; hg19: chrX-102579116;