rs5918294

Positions:

• chrX-42110232-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.31 in 110,580 control chromosomes in the GnomAD database, including 4,222 homozygotes. There are 9,908 hemizygotes in GnomAD. 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 0.31 (4222 hom., 9908 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.572

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

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: 0.311 AC: 34322 AN: 110530 Hom.: 4221 Cov.: 23 AF XY: 0.302 AC XY: 9898 AN XY: 32790

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.313

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.310 AC: 34334 AN: 110580 Hom.: 4222 Cov.: 23 AF XY: 0.302 AC XY: 9908 AN XY: 32854

Gnomad4 AFR AF: 0.181

Gnomad4 AMR AF: 0.367

Gnomad4 ASJ AF: 0.414

Gnomad4 EAS AF: 0.154

Gnomad4 SAS AF: 0.244

Gnomad4 FIN AF: 0.337

Gnomad4 NFE AF: 0.380

Gnomad4 OTH AF: 0.314

Alfa AF: 0.365 Hom.: 32837

Bravo AF: 0.303

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.084
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5918294; hg19: chrX-41969485;