rs1876458

Positions:

• chrX-22520453-A-G

Variant summary

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

The NR_073010.2(PTCHD1-AS):​n.454-130733T>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 NR_073010.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.915

Genes affected

ENSG00000289084 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTCHD1-AS	NR_073010.2	n.454-130733T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000289084	ENST00000687119.1	n.312+100471T>C		intron_variant
ENSG00000289084	ENST00000687248.1	n.454-130733T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.150 AC: 16761 AN: 111781 Hom.: 953 Cov.: 23 AF XY: 0.140 AC XY: 4750 AN XY: 34015

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

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.140

Gnomad4 ASJ AF: 0.203

Gnomad4 EAS AF: 0.0456

Gnomad4 SAS AF: 0.214

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.178

Gnomad4 OTH AF: 0.179

Alfa AF: 0.175 Hom.: 8994

Bravo AF: 0.152

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.9
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1876458; hg19: chrX-22538570;