rs12687176

Variant names:

• chrX-123859028-C-T
• rs12687176

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 0.169 in 110,589 control chromosomes in the GnomAD database, including 1,255 homozygotes. There are 5,725 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 0.17 (1255 hom., 5725 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.103

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.345 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: 0.169 AC: 18666 AN: 110538 Hom.: 1252 Cov.: 22 AF XY: 0.175 AC XY: 5721 AN XY: 32764

Gnomad AFR AF: 0.0685

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.243

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.169 AC: 18673 AN: 110589 Hom.: 1255 Cov.: 22 AF XY: 0.174 AC XY: 5725 AN XY: 32825

Gnomad4 AFR AF: 0.0685

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.177

Gnomad4 EAS AF: 0.333

Gnomad4 SAS AF: 0.364

Gnomad4 FIN AF: 0.246

Gnomad4 NFE AF: 0.189

Gnomad4 OTH AF: 0.190

Alfa AF: 0.166 Hom.: 1148

Bravo AF: 0.164

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.5
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12687176; hg19: chrX-122992878;