X-23215224-C-T

Position:

• chrX-23215224-C-T

Variant summary

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

The NR_073010.2(PTCHD1-AS):​n.259+54827G>A variant causes a intron, non coding transcript 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 NR_073010.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0150

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
PTCHD1-AS	NR_073010.2	n.259+54827G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000687248.1	n.259+54827G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.285 AC: 31449 AN: 110487 Hom.: 3260 Cov.: 22 AF XY: 0.284 AC XY: 9308 AN XY: 32739

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

Gnomad4 AFR AF: 0.243

Gnomad4 AMR AF: 0.418

Gnomad4 ASJ AF: 0.244

Gnomad4 EAS AF: 0.478

Gnomad4 SAS AF: 0.367

Gnomad4 FIN AF: 0.251

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.308

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs718156; hg19: chrX-23233341;