rs3116754

Variant names:

• chrX-129641598-T-A
• rs3116754

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 0.303 in 110,474 control chromosomes in the GnomAD database, including 7,511 homozygotes. There are 9,442 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 0.30 (7511 hom., 9442 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.861

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 (AFR) allele frequency at 95% confidence interval = 0.755 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: 0.303 AC: 33474 AN: 110421 Hom.: 7504 Cov.: 22 AF XY: 0.287 AC XY: 9394 AN XY: 32733

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.0956

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.0569

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0737

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.303 AC: 33527 AN: 110474 Hom.: 7511 Cov.: 22 AF XY: 0.288 AC XY: 9442 AN XY: 32796

Gnomad4 AFR AF: 0.763

Gnomad4 AMR AF: 0.258

Gnomad4 ASJ AF: 0.0956

Gnomad4 EAS AF: 0.689

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.0569

Gnomad4 NFE AF: 0.0737

Gnomad4 OTH AF: 0.272

Alfa AF: 0.0153 Hom.: 54

Bravo AF: 0.350

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.3
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3116754; hg19: chrX-128775575;