rs12843815

chrX-151853928-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 0.477 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/exons	MANE	UniProt

Ensembl

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