rs3116754

Positions:

• chrX-129641598-T-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;