rs12687176

Variant names:

• chrX-123859028-C-T
• rs12687176

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.169 AC: 18666 AN: 110538 Hom.: 1252 Cov.: 22

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

African (AFR) AF: 0.0685 AC: 2095 AN: 30571

American (AMR) AF: 0.210 AC: 2170 AN: 10346

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 466 AN: 2639

East Asian (EAS) AF: 0.333 AC: 1162 AN: 3486

South Asian (SAS) AF: 0.364 AC: 945 AN: 2594

European-Finnish (FIN) AF: 0.246 AC: 1422 AN: 5771

Middle Eastern (MID) AF: 0.252 AC: 54 AN: 214

European-Non Finnish (NFE) AF: 0.189 AC: 9959 AN: 52772

Other (OTH) AF: 0.190 AC: 291 AN: 1528

Alfa AF: 0.166 Hom.: 1148

Bravo AF: 0.164

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.5
DANN	Benign	0.79
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs12687176; hg19: chrX-122992878;