X-134251303-C-T

Variant names:

• chrX-134251303-C-T
• rs5975453

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 0.165 in 108,277 control chromosomes in the GnomAD database, including 1,332 homozygotes. There are 5,115 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 0.16 (1332 hom., 5115 hem., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.404 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: 0.165 AC: 17814 AN: 108228 Hom.: 1331 Cov.: 21 AF XY: 0.167 AC XY: 5105 AN XY: 30638

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.0622

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.0712

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.0976

Gnomad MID AF: 0.0819

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.165 AC: 17829 AN: 108277 Hom.: 1332 Cov.: 21 AF XY: 0.167 AC XY: 5115 AN XY: 30697

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.352

Gnomad4 ASJ AF: 0.0712

Gnomad4 EAS AF: 0.423

Gnomad4 SAS AF: 0.293

Gnomad4 FIN AF: 0.0976

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.178

Alfa AF: 0.137 Hom.: 2469

Bravo AF: 0.194

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.3
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5975453; hg19: chrX-133385333;