rs12393443

Variant names:

• chrX-51784996-T-G
• rs12393443

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 0.132 in 111,075 control chromosomes in the GnomAD database, including 812 homozygotes. There are 4,199 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 0.13 (812 hom., 4199 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.173 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: 0.132 AC: 14613 AN: 111024 Hom.: 809 Cov.: 23

Gnomad AFR AF: 0.0618

Gnomad AMI AF: 0.0991

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.0395

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.145

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.132 AC: 14627 AN: 111075 Hom.: 812 Cov.: 23 AF XY: 0.126 AC XY: 4199 AN XY: 33267

African (AFR) AF: 0.0621 AC: 1901 AN: 30595

American (AMR) AF: 0.114 AC: 1191 AN: 10470

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 339 AN: 2634

East Asian (EAS) AF: 0.0394 AC: 139 AN: 3530

South Asian (SAS) AF: 0.135 AC: 355 AN: 2622

European-Finnish (FIN) AF: 0.182 AC: 1075 AN: 5917

Middle Eastern (MID) AF: 0.159 AC: 34 AN: 214

European-Non Finnish (NFE) AF: 0.176 AC: 9315 AN: 52906

Other (OTH) AF: 0.140 AC: 211 AN: 1511

Alfa AF: 0.169 Hom.: 2552

Bravo AF: 0.126

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.9
DANN	Benign	0.67
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs12393443; hg19: chrX-51528092;