X-43753072-C-T

Variant names:

• chrX-43753072-C-T
• rs12843533

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 0.0691 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0691 AC: 7749 AN: 112075 Hom.: 285 Cov.: 23

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

African (AFR) AF: 0.0190 AC: 589 AN: 30971

American (AMR) AF: 0.0422 AC: 446 AN: 10573

Ashkenazi Jewish (ASJ) AF: 0.0476 AC: 126 AN: 2649

East Asian (EAS) AF: 0.000840 AC: 3 AN: 3571

South Asian (SAS) AF: 0.0143 AC: 39 AN: 2723

European-Finnish (FIN) AF: 0.116 AC: 700 AN: 6049

Middle Eastern (MID) AF: 0.00461 AC: 1 AN: 217

European-Non Finnish (NFE) AF: 0.106 AC: 5654 AN: 53162

Other (OTH) AF: 0.0439 AC: 67 AN: 1526

Alfa AF: 0.0432 Hom.: 440

Bravo AF: 0.0608

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.28
DANN	Benign	0.72
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs12843533; hg19: chrX-43612319;