rs12555969

Positions:

• chrX-146302374-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 0.36 in 110,039 control chromosomes in the GnomAD database, including 5,805 homozygotes. There are 11,849 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 0.36 (5805 hom., 11849 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.27

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.505 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.360 AC: 39621 AN: 109987 Hom.: 5799 Cov.: 22 AF XY: 0.367 AC XY: 11838 AN XY: 32237

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.360 AC: 39640 AN: 110039 Hom.: 5805 Cov.: 22 AF XY: 0.367 AC XY: 11849 AN XY: 32299

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.517

Gnomad4 ASJ AF: 0.425

Gnomad4 EAS AF: 0.462

Gnomad4 SAS AF: 0.359

Gnomad4 FIN AF: 0.549

Gnomad4 NFE AF: 0.421

Gnomad4 OTH AF: 0.391

Alfa AF: 0.419 Hom.: 20802

Bravo AF: 0.358

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.051
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12555969; hg19: chrX-145383892;