X-23288726-A-G

Variant names:

• chrX-23288726-A-G
• rs4828980
• ENST00000687248.2:n.161+4288T>C

Variant summary

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

The ENST00000687248.2(PTCHD1-AS):​n.161+4288T>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 0.65 (19438 hom., 21308 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: PTCHD1-AS ENST00000687248.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.358
• Publications: 1 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=-0.79).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTCHD1-AS	NR_073010.2	n.133+4288T>C		intron_variant	Intron 1 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTCHD1-AS	ENST00000687248.2	n.161+4288T>C		intron_variant	Intron 1 of 8
PTCHD1-AS	ENST00000799269.1	n.410-18550T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.655 AC: 72462 AN: 110633 Hom.: 19447 Cov.: 23

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.881

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.809

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.884

Gnomad MID AF: 0.694

Gnomad NFE AF: 0.867

Gnomad OTH AF: 0.677

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: 0.655 AC: 72460 AN: 110685 Hom.: 19438 Cov.: 23 AF XY: 0.648 AC XY: 21308 AN XY: 32905

African (AFR) AF: 0.289 AC: 8820 AN: 30546

American (AMR) AF: 0.574 AC: 5969 AN: 10392

Ashkenazi Jewish (ASJ) AF: 0.809 AC: 2130 AN: 2634

East Asian (EAS) AF: 0.478 AC: 1669 AN: 3489

South Asian (SAS) AF: 0.445 AC: 1145 AN: 2573

European-Finnish (FIN) AF: 0.884 AC: 5115 AN: 5783

Middle Eastern (MID) AF: 0.668 AC: 141 AN: 211

European-Non Finnish (NFE) AF: 0.867 AC: 45853 AN: 52874

Other (OTH) AF: 0.678 AC: 1019 AN: 1503

Alfa AF: 0.762 Hom.: 50208

Bravo AF: 0.619

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.1
DANN	Benign	0.62
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs4828980; hg19: chrX-23306843;