rs5926214

Positions:

• chrX-22517291-G-A

Variant summary

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

The NR_073010.2(PTCHD1-AS):​n.454-127571C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 110,069 control chromosomes in the GnomAD database, including 4,997 homozygotes. There are 11,238 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 0.35 (4997 hom., 11238 hem., cov: 22)
• Consequence: PTCHD1-AS NR_073010.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.09

Genes affected

ENSG00000289084 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTCHD1-AS	NR_073010.2	n.454-127571C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000289084	ENST00000687119.1	n.312+103633C>T		intron_variant
ENSG00000289084	ENST00000687248.1	n.454-127571C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.351 AC: 38572 AN: 110014 Hom.: 4998 Cov.: 22 AF XY: 0.346 AC XY: 11193 AN XY: 32332

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.432

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.351 AC: 38608 AN: 110069 Hom.: 4997 Cov.: 22 AF XY: 0.347 AC XY: 11238 AN XY: 32397

Gnomad4 AFR AF: 0.441

Gnomad4 AMR AF: 0.310

Gnomad4 ASJ AF: 0.384

Gnomad4 EAS AF: 0.352

Gnomad4 SAS AF: 0.509

Gnomad4 FIN AF: 0.279

Gnomad4 NFE AF: 0.304

Gnomad4 OTH AF: 0.385

Alfa AF: 0.330 Hom.: 7358

Bravo AF: 0.355

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	7.9
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5926214; hg19: chrX-22535408;