rs12388359

chrX-10263651-G-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, non coding transcript 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: ENST00000454113.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.266

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000454113.1	n.495+710G>T		intron_variant, non_coding_transcript_variant		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;