X-23082228-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.260-18107G>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 0.391 in 110,436 control chromosomes in the GnomAD database, including 6,946 homozygotes. There are 12,359 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 0.39 (6946 hom., 12359 hem., cov: 22)
• Consequence: PTCHD1-AS NR_073010.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.597 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTCHD1-AS	NR_073010.2	n.260-18107G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000687248.1	n.260-18107G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.391 AC: 43179 AN: 110380 Hom.: 6947 Cov.: 22 AF XY: 0.377 AC XY: 12324 AN XY: 32684

Gnomad AFR AF: 0.605

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.391 AC: 43211 AN: 110436 Hom.: 6946 Cov.: 22 AF XY: 0.377 AC XY: 12359 AN XY: 32750

Gnomad4 AFR AF: 0.605

Gnomad4 AMR AF: 0.348

Gnomad4 ASJ AF: 0.346

Gnomad4 EAS AF: 0.456

Gnomad4 SAS AF: 0.353

Gnomad4 FIN AF: 0.351

Gnomad4 NFE AF: 0.283

Gnomad4 OTH AF: 0.361

Alfa AF: 0.366 Hom.: 2593

Bravo AF: 0.406

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.81
Dann	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16982419; hg19: chrX-23100345;