X-48537494-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

ENSG00000286268 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000651615.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286268	ENST00000651615.1		c.540+1456C>T		intron	N/A	ENSP00000498524.1	A0A494C0F3

Frequencies

GnomAD3 genomes AF: 0.297 AC: 32598 AN: 109819 Hom.: 3773 Cov.: 22

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

African (AFR) AF: 0.197 AC: 5959 AN: 30209

American (AMR) AF: 0.324 AC: 3330 AN: 10264

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 522 AN: 2639

East Asian (EAS) AF: 0.439 AC: 1532 AN: 3490

South Asian (SAS) AF: 0.307 AC: 806 AN: 2622

European-Finnish (FIN) AF: 0.376 AC: 2104 AN: 5602

Middle Eastern (MID) AF: 0.156 AC: 33 AN: 212

European-Non Finnish (NFE) AF: 0.337 AC: 17714 AN: 52638

Other (OTH) AF: 0.285 AC: 430 AN: 1507

Alfa AF: 0.316 Hom.: 13927

Bravo AF: 0.290

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.17
DANN	Benign	0.27
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs11795513; hg19: chrX-48395882;