X-48537494-C-T

Variant names:

• chrX-48537494-C-T
• rs11795513
• ENST00000651615.1:c.540+1456C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000651615.1(ENSG00000286268):​c.540+1456C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 109,852 control chromosomes in the GnomAD database, including 3,779 homozygotes. There are 9,417 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 0.30 (3779 hom., 9417 hem., cov: 22)
• Consequence: ENSG00000286268 ENST00000651615.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.597

Genes affected

ENSG00000286268 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.421 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
ENSG00000286268	ENST00000651615.1	c.540+1456C>T		intron_variant	Intron 5 of 6			ENSP00000498524.1

Frequencies

GnomAD3 genomes AF: 0.297 AC: 32598 AN: 109819 Hom.: 3773 Cov.: 22 AF XY: 0.292 AC XY: 9406 AN XY: 32163

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.297 AC: 32619 AN: 109852 Hom.: 3779 Cov.: 22 AF XY: 0.292 AC XY: 9417 AN XY: 32208

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.439

Gnomad4 SAS AF: 0.307

Gnomad4 FIN AF: 0.376

Gnomad4 NFE AF: 0.337

Gnomad4 OTH AF: 0.285

Alfa AF: 0.324 Hom.: 9908

Bravo AF: 0.290

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.17
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: rs11795513; hg19: chrX-48395882;