rs12843815

Variant names:

• chrX-151853928-C-T
• rs12843815

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.477 AC: 52652 AN: 110462 Hom.: 9055 Cov.: 23

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

African (AFR) AF: 0.533 AC: 16190 AN: 30354

American (AMR) AF: 0.505 AC: 5279 AN: 10445

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 1119 AN: 2634

East Asian (EAS) AF: 0.399 AC: 1380 AN: 3459

South Asian (SAS) AF: 0.423 AC: 1069 AN: 2526

European-Finnish (FIN) AF: 0.402 AC: 2397 AN: 5964

Middle Eastern (MID) AF: 0.479 AC: 103 AN: 215

European-Non Finnish (NFE) AF: 0.458 AC: 24192 AN: 52768

Other (OTH) AF: 0.485 AC: 721 AN: 1486

Alfa AF: 0.466 Hom.: 60917

Bravo AF: 0.484

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.5
DANN	Benign	0.68
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs12843815; hg19: chrX-151022400;