rs5918139

Variant names:

• chrX-41257277-T-C
• rs5918139

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 0.241 in 110,581 control chromosomes in the GnomAD database, including 2,786 homozygotes. There are 7,629 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 0.24 (2786 hom., 7629 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.241 AC: 26622 AN: 110528 Hom.: 2779 Cov.: 23 AF XY: 0.232 AC XY: 7596 AN XY: 32798

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.241 AC: 26668 AN: 110581 Hom.: 2786 Cov.: 23 AF XY: 0.232 AC XY: 7629 AN XY: 32861

Gnomad4 AFR AF: 0.375

Gnomad4 AMR AF: 0.239

Gnomad4 ASJ AF: 0.190

Gnomad4 EAS AF: 0.402

Gnomad4 SAS AF: 0.242

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.240

Alfa AF: 0.181 Hom.: 13849

Bravo AF: 0.257

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.4
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5918139; hg19: chrX-41116530;