rs929095

chrX-43503701-C-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 0.55 (13206 hom., 18175 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.595

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS2: High Homozygotes in GnomAd at 13210 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: 0.553 AC: 61080 AN: 110510 Hom.: 13210 Cov.: 23 AF XY: 0.554 AC XY: 18154 AN XY: 32780

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.528

Gnomad AMR AF: 0.696

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.582

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.653

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.569

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: 0.553 AC: 61093 AN: 110559 Hom.: 13206 Cov.: 23 AF XY: 0.553 AC XY: 18175 AN XY: 32839

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.696

Gnomad4 ASJ AF: 0.579

Gnomad4 EAS AF: 0.583

Gnomad4 SAS AF: 0.451

Gnomad4 FIN AF: 0.696

Gnomad4 NFE AF: 0.675

Gnomad4 OTH AF: 0.568

Alfa AF: 0.607 Hom.: 4712

Bravo AF: 0.545

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.76
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs929095; hg19: chrX-43362950; COSMIC: COSV68315919;