rs1876458

Variant names:

• chrX-22520453-A-G
• rs1876458
• ENST00000687119.1:n.312+100471T>C

Variant summary

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

The ENST00000687119.1(PTCHD1-AS):​n.312+100471T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 111,833 control chromosomes in the GnomAD database, including 951 homozygotes. There are 4,767 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 0.15 (951 hom., 4767 hem., cov: 23)
• Consequence: PTCHD1-AS ENST00000687119.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.915
• 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=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000687119.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTCHD1-AS	NR_073010.2		n.454-130733T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTCHD1-AS	ENST00000687119.1		n.312+100471T>C		intron	N/A
	PTCHD1-AS	ENST00000687248.2		n.482-130733T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.150 AC: 16761 AN: 111781 Hom.: 953 Cov.: 23

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.0454

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.150 AC: 16772 AN: 111833 Hom.: 951 Cov.: 23 AF XY: 0.140 AC XY: 4767 AN XY: 34077

African (AFR) AF: 0.113 AC: 3474 AN: 30821

American (AMR) AF: 0.140 AC: 1481 AN: 10541

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 537 AN: 2648

East Asian (EAS) AF: 0.0456 AC: 163 AN: 3577

South Asian (SAS) AF: 0.214 AC: 579 AN: 2707

European-Finnish (FIN) AF: 0.117 AC: 716 AN: 6099

Middle Eastern (MID) AF: 0.153 AC: 33 AN: 216

European-Non Finnish (NFE) AF: 0.178 AC: 9424 AN: 53021

Other (OTH) AF: 0.179 AC: 272 AN: 1521

Alfa AF: 0.172 Hom.: 12574

Bravo AF: 0.152

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.9
DANN	Benign	0.60
PhyloP100		0.92
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs1876458; hg19: chrX-22538570;