X-23218935-C-T

Variant names:

• chrX-23218935-C-T
• rs1557902
• ENST00000687248.2:n.287+51116G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000687248.2(PTCHD1-AS):​n.287+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 ENST00000687248.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.772
• Publications: 0 publications found

Genes affected

PTCHD1-AS (HGNC:37703): (PTCHD1 antisense RNA (head to head))

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PTCHD1-AS	NR_073010.2	n.259+51116G>A		intron_variant	Intron 2 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTCHD1-AS	ENST00000687248.2	n.287+51116G>A		intron_variant	Intron 2 of 8

Frequencies

GnomAD3 genomes AF: 0.250 AC: 27814 AN: 111080 Hom.: 2794 Cov.: 23

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

African (AFR) AF: 0.131 AC: 4041 AN: 30777

American (AMR) AF: 0.397 AC: 4115 AN: 10378

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 610 AN: 2628

East Asian (EAS) AF: 0.478 AC: 1682 AN: 3519

South Asian (SAS) AF: 0.361 AC: 953 AN: 2640

European-Finnish (FIN) AF: 0.243 AC: 1434 AN: 5900

Middle Eastern (MID) AF: 0.230 AC: 49 AN: 213

European-Non Finnish (NFE) AF: 0.271 AC: 14321 AN: 52885

Other (OTH) AF: 0.279 AC: 423 AN: 1515

Alfa AF: 0.254 Hom.: 11063

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
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs1557902; hg19: chrX-23237052;