rs12388359

Variant names:

• chrX-10263651-G-T
• rs12388359
• ENST00000454113.1:n.495+710G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000454113.1(ENSG00000227042):​n.495+710G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 110,162 control chromosomes in the GnomAD database, including 1,800 homozygotes. There are 5,675 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 0.19 (1800 hom., 5675 hem., cov: 22)
• Consequence: ENSG00000227042 ENST00000454113.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.266
• Publications: 11 publications found

Genes affected

ENSG00000227042 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.328 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
ENSG00000227042	ENST00000454113.1	n.495+710G>T		intron_variant	Intron 3 of 4	3

Frequencies

GnomAD3 genomes AF: 0.187 AC: 20618 AN: 110115 Hom.: 1799 Cov.: 22

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.0969

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.187 AC: 20638 AN: 110162 Hom.: 1800 Cov.: 22 AF XY: 0.175 AC XY: 5675 AN XY: 32496

African (AFR) AF: 0.333 AC: 10041 AN: 30146

American (AMR) AF: 0.115 AC: 1190 AN: 10318

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 507 AN: 2628

East Asian (EAS) AF: 0.105 AC: 368 AN: 3505

South Asian (SAS) AF: 0.0957 AC: 245 AN: 2560

European-Finnish (FIN) AF: 0.150 AC: 868 AN: 5790

Middle Eastern (MID) AF: 0.194 AC: 42 AN: 217

European-Non Finnish (NFE) AF: 0.132 AC: 6991 AN: 52815

Other (OTH) AF: 0.180 AC: 272 AN: 1507

Alfa AF: 0.154 Hom.: 11995

Bravo AF: 0.195

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.27
PhyloP100		0.27
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs12388359; hg19: chrX-10231691;