X-22873960-A-G

Position:

• chrX-22873960-A-G

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NR_073010.2(PTCHD1-AS):​n.344-130622T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. 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 0.74 (21638 hom., 23591 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: PTCHD1-AS NR_073010.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.317

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTCHD1-AS	NR_073010.2	n.344-130622T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000687248.1	n.344-130622T>C		intron_variant, non_coding_transcript_variant
	ENST00000687119.1	n.178+70093T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.743 AC: 81133 AN: 109184 Hom.: 21637 Cov.: 22 AF XY: 0.745 AC XY: 23532 AN XY: 31580

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.797

Gnomad AMR AF: 0.782

Gnomad ASJ AF: 0.741

Gnomad EAS AF: 0.868

Gnomad SAS AF: 0.874

Gnomad FIN AF: 0.661

Gnomad MID AF: 0.795

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.741

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.743 AC: 81189 AN: 109232 Hom.: 21638 Cov.: 22 AF XY: 0.746 AC XY: 23591 AN XY: 31638

Gnomad4 AFR AF: 0.838

Gnomad4 AMR AF: 0.782

Gnomad4 ASJ AF: 0.741

Gnomad4 EAS AF: 0.868

Gnomad4 SAS AF: 0.873

Gnomad4 FIN AF: 0.661

Gnomad4 NFE AF: 0.675

Gnomad4 OTH AF: 0.744

Alfa AF: 0.664 Hom.: 13880

Bravo AF: 0.753

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.7
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5925696; hg19: chrX-22892077;