ENST00000687119.1:n.178+70093T>C

Variant names:

• chrX-22873960-A-G
• rs5925696
• ENST00000687119.1:n.178+70093T>C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000687119.1(PTCHD1-AS):​n.178+70093T>C variant causes a intron 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 ENST00000687119.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.317
• Publications: 6 publications found

Genes affected

PTCHD1-AS (HGNC:37703): (PTCHD1 antisense RNA (head to head))

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000687119.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTCHD1-AS	NR_073010.2		n.344-130622T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTCHD1-AS	ENST00000687119.1		n.178+70093T>C		intron	N/A
	PTCHD1-AS	ENST00000687248.2		n.372-130622T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.743 AC: 81133 AN: 109184 Hom.: 21637 Cov.: 22

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

African (AFR) AF: 0.838 AC: 25234 AN: 30119

American (AMR) AF: 0.782 AC: 7947 AN: 10162

Ashkenazi Jewish (ASJ) AF: 0.741 AC: 1947 AN: 2626

East Asian (EAS) AF: 0.868 AC: 2944 AN: 3393

South Asian (SAS) AF: 0.873 AC: 2252 AN: 2579

European-Finnish (FIN) AF: 0.661 AC: 3666 AN: 5548

Middle Eastern (MID) AF: 0.785 AC: 164 AN: 209

European-Non Finnish (NFE) AF: 0.675 AC: 35385 AN: 52426

Other (OTH) AF: 0.744 AC: 1115 AN: 1499

Alfa AF: 0.708 Hom.: 25987

Bravo AF: 0.753

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.7
DANN	Benign	0.83
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs5925696; hg19: chrX-22892077;