rs12014367

Positions:

• chrX-79619424-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;