rs1558022

chrX-117374356-C-T

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 0.65 (17200 hom., 22014 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00100

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BS2: High Homozygotes in GnomAd at 17192 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: 0.652 AC: 72374 AN: 111060 Hom.: 17192 Cov.: 23 AF XY: 0.659 AC XY: 21961 AN XY: 33302

Gnomad AFR AF: 0.814

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.742

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.858

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.523

Gnomad OTH AF: 0.632

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: 72430 AN: 111110 Hom.: 17200 Cov.: 23 AF XY: 0.660 AC XY: 22014 AN XY: 33362

Gnomad4 AFR AF: 0.814

Gnomad4 AMR AF: 0.742

Gnomad4 ASJ AF: 0.565

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.856

Gnomad4 FIN AF: 0.575

Gnomad4 NFE AF: 0.523

Gnomad4 OTH AF: 0.638

Alfa AF: 0.584 Hom.: 14569

Bravo AF: 0.673

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.4
Dann	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1558022; hg19: chrX-116508319;