rs12843815

Variant names:

• chrX-151853928-C-T
• rs12843815

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 0.477 in 110,521 control chromosomes in the GnomAD database, including 9,053 homozygotes. There are 15,449 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 0.48 (9053 hom., 15449 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.526 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: 0.477 AC: 52652 AN: 110462 Hom.: 9055 Cov.: 23 AF XY: 0.471 AC XY: 15413 AN XY: 32730

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.477 AC: 52674 AN: 110521 Hom.: 9053 Cov.: 23 AF XY: 0.471 AC XY: 15449 AN XY: 32799

Gnomad4 AFR AF: 0.533

Gnomad4 AMR AF: 0.505

Gnomad4 ASJ AF: 0.425

Gnomad4 EAS AF: 0.399

Gnomad4 SAS AF: 0.423

Gnomad4 FIN AF: 0.402

Gnomad4 NFE AF: 0.458

Gnomad4 OTH AF: 0.485

Alfa AF: 0.462 Hom.: 50015

Bravo AF: 0.484

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.5
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12843815; hg19: chrX-151022400;