X-23288726-A-G

Position:

• chrX-23288726-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.133+4288T>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 0.65 (19438 hom., 21308 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: PTCHD1-AS NR_073010.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.358

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTCHD1-AS	NR_073010.2	n.133+4288T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000687248.1	n.133+4288T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.655 AC: 72462 AN: 110633 Hom.: 19447 Cov.: 23 AF XY: 0.648 AC XY: 21287 AN XY: 32843

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

Gnomad4 AFR AF: 0.289

Gnomad4 AMR AF: 0.574

Gnomad4 ASJ AF: 0.809

Gnomad4 EAS AF: 0.478

Gnomad4 SAS AF: 0.445

Gnomad4 FIN AF: 0.884

Gnomad4 NFE AF: 0.867

Gnomad4 OTH AF: 0.678

Alfa AF: 0.787 Hom.: 37159

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4828980; hg19: chrX-23306843;