rs2202091

chrX-146004438-C-AchrX-146004438-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 0.60 (14349 hom., 17793 hem., cov: 21)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.652

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BS2: High Homozygotes in GnomAd at 14338 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: 0.599 AC: 64367 AN: 107420 Hom.: 14338 Cov.: 21 AF XY: 0.593 AC XY: 17752 AN XY: 29938

Gnomad AFR AF: 0.737

Gnomad AMI AF: 0.417

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.590

Gnomad SAS AF: 0.639

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.586

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.572

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: 0.599 AC: 64413 AN: 107463 Hom.: 14349 Cov.: 21 AF XY: 0.593 AC XY: 17793 AN XY: 29991

Gnomad4 AFR AF: 0.737

Gnomad4 AMR AF: 0.554

Gnomad4 ASJ AF: 0.437

Gnomad4 EAS AF: 0.590

Gnomad4 SAS AF: 0.637

Gnomad4 FIN AF: 0.551

Gnomad4 NFE AF: 0.545

Gnomad4 OTH AF: 0.575

Alfa AF: 0.577 Hom.: 4341

Bravo AF: 0.606

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.0
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2202091; hg19: chrX-145085956;