X-43753072-C-T

Variant names:

• chrX-43753072-C-T
• rs12843533

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 0.0691 in 112,125 control chromosomes in the GnomAD database, including 285 homozygotes. There are 2,232 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 0.069 (285 hom., 2232 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.997

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 (NFE) allele frequency at 95% confidence interval = 0.104 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: 0.0691 AC: 7749 AN: 112075 Hom.: 285 Cov.: 23 AF XY: 0.0652 AC XY: 2232 AN XY: 34249

Gnomad AFR AF: 0.0191

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.0422

Gnomad ASJ AF: 0.0476

Gnomad EAS AF: 0.000837

Gnomad SAS AF: 0.0143

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.00420

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.0445

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

GnomAD4 genome AF: 0.0691 AC: 7750 AN: 112125 Hom.: 285 Cov.: 23 AF XY: 0.0651 AC XY: 2232 AN XY: 34309

Gnomad4 AFR AF: 0.0190

Gnomad4 AMR AF: 0.0422

Gnomad4 ASJ AF: 0.0476

Gnomad4 EAS AF: 0.000840

Gnomad4 SAS AF: 0.0143

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.106

Gnomad4 OTH AF: 0.0439

Alfa AF: 0.0556 Hom.: 376

Bravo AF: 0.0608

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.28
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12843533; hg19: chrX-43612319;