rs12014367

Variant names:

• chrX-79619424-C-T
• rs12014367

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 0.173 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.173 AC: 19088 AN: 110352 Hom.: 1353 Cov.: 22 AF XY: 0.166 AC XY: 5421 AN XY: 32654

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

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.118

Gnomad4 SAS AF: 0.245

Gnomad4 FIN AF: 0.213

Gnomad4 NFE AF: 0.209

Gnomad4 OTH AF: 0.180

Alfa AF: 0.201 Hom.: 3691

Bravo AF: 0.165

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12014367; hg19: chrX-78874921;