rs12014367

Variant names:

• chrX-79619424-C-T
• rs12014367

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 0.173 in 110,400 control chromosomes in the GnomAD database, including 1,351 homozygotes. There are 5,432 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 (1351 hom., 5432 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.555
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.229 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: 0.173 AC: 19088 AN: 110352 Hom.: 1353 Cov.: 22

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.173 AC: 19095 AN: 110400 Hom.: 1351 Cov.: 22 AF XY: 0.166 AC XY: 5432 AN XY: 32712

African (AFR) AF: 0.108 AC: 3288 AN: 30529

American (AMR) AF: 0.129 AC: 1332 AN: 10290

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 484 AN: 2632

East Asian (EAS) AF: 0.118 AC: 410 AN: 3482

South Asian (SAS) AF: 0.245 AC: 650 AN: 2658

European-Finnish (FIN) AF: 0.213 AC: 1208 AN: 5682

Middle Eastern (MID) AF: 0.244 AC: 52 AN: 213

European-Non Finnish (NFE) AF: 0.209 AC: 11048 AN: 52754

Other (OTH) AF: 0.180 AC: 269 AN: 1495

Alfa AF: 0.202 Hom.: 4134

Bravo AF: 0.165

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.3
DANN	Benign	0.67
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs12014367; hg19: chrX-78874921;