rs177008

chrX-125567397-A-G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

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 (17259 hom., 21444 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BS2: High Homozygotes in GnomAd at 17259 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.664 AC: 73116 AN: 110069 Hom.: 17259 Cov.: 22 AF XY: 0.662 AC XY: 21398 AN XY: 32341

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.897

Gnomad SAS AF: 0.723

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.676

Gnomad OTH AF: 0.671

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: 0.664 AC: 73155 AN: 110119 Hom.: 17259 Cov.: 22 AF XY: 0.662 AC XY: 21444 AN XY: 32401

Gnomad4 AFR AF: 0.600

Gnomad4 AMR AF: 0.697

Gnomad4 ASJ AF: 0.687

Gnomad4 EAS AF: 0.897

Gnomad4 SAS AF: 0.724

Gnomad4 FIN AF: 0.669

Gnomad4 NFE AF: 0.676

Gnomad4 OTH AF: 0.672

Alfa AF: 0.678 Hom.: 53808

Bravo AF: 0.666

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.74
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs177008; hg19: chrX-124701246;