X-23218935-C-T

Position:

• chrX-23218935-C-T

Variant summary

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

The NR_073010.2(PTCHD1-AS):​n.259+51116G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 111,130 control chromosomes in the GnomAD database, including 2,797 homozygotes. There are 8,325 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 0.25 (2797 hom., 8325 hem., cov: 23)
• Consequence: PTCHD1-AS NR_073010.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.772

Genes affected

ENSG00000289084 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.459 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTCHD1-AS	NR_073010.2	n.259+51116G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000289084	ENST00000687248.1	n.259+51116G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.250 AC: 27814 AN: 111080 Hom.: 2794 Cov.: 23 AF XY: 0.249 AC XY: 8305 AN XY: 33336

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.250 AC: 27835 AN: 111130 Hom.: 2797 Cov.: 23 AF XY: 0.249 AC XY: 8325 AN XY: 33398

Gnomad4 AFR AF: 0.131

Gnomad4 AMR AF: 0.397

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.478

Gnomad4 SAS AF: 0.361

Gnomad4 FIN AF: 0.243

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.279

Alfa AF: 0.250 Hom.: 9298

Bravo AF: 0.266

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.21
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1557902; hg19: chrX-23237052;