rs12388359

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000227042 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 AF XY: 0.174 AC XY: 5660 AN XY: 32439

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

Gnomad4 AFR AF: 0.333

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.105

Gnomad4 SAS AF: 0.0957

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.180

Alfa AF: 0.141 Hom.: 8409

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12388359; hg19: chrX-10231691;