rs718156

Variant names:

• chrX-23215224-C-T
• rs718156
• ENST00000687248.2:n.287+54827G>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+54827G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 110,543 control chromosomes in the GnomAD database, including 3,264 homozygotes. There are 9,341 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 0.28 (3264 hom., 9341 hem., cov: 22)
• Consequence: PTCHD1-AS ENST00000687248.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0150
• Publications: 1 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=-0.94).
• 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+54827G>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+54827G>A		intron_variant	Intron 2 of 8

Frequencies

GnomAD3 genomes AF: 0.285 AC: 31449 AN: 110487 Hom.: 3260 Cov.: 22

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.285 AC: 31481 AN: 110543 Hom.: 3264 Cov.: 22 AF XY: 0.285 AC XY: 9341 AN XY: 32805

African (AFR) AF: 0.243 AC: 7386 AN: 30416

American (AMR) AF: 0.418 AC: 4356 AN: 10425

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 643 AN: 2640

East Asian (EAS) AF: 0.478 AC: 1645 AN: 3440

South Asian (SAS) AF: 0.367 AC: 933 AN: 2545

European-Finnish (FIN) AF: 0.251 AC: 1478 AN: 5892

Middle Eastern (MID) AF: 0.254 AC: 54 AN: 213

European-Non Finnish (NFE) AF: 0.271 AC: 14316 AN: 52795

Other (OTH) AF: 0.308 AC: 464 AN: 1505

Alfa AF: 0.287 Hom.: 2138

Bravo AF: 0.304

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.60
DANN	Benign	0.21
PhyloP100		0.015

Splicing

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

Other links and lift over

dbSNP: rs718156; hg19: chrX-23233341;