X-43753072-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 0.0691 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/exons	MANE	UniProt

Ensembl

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