rs5925651

Variant names:

• chrX-22651114-C-A
• rs5925651
• ENST00000687119.1:n.179-30057G>T

Your query was ambiguous. Multiple possible variants found:

• chrX-22651114-C-A
• chrX-22651114-C-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_073010.2(PTCHD1-AS):​n.453+92115G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 111,585 control chromosomes in the GnomAD database, including 2,417 homozygotes. There are 7,600 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 0.23 (2417 hom., 7600 hem., cov: 23)
• Consequence: PTCHD1-AS NR_073010.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.726

Genes affected

ENSG00000289084 (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.335 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTCHD1-AS	NR_073010.2	n.453+92115G>T		intron_variant	Intron 4 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289084	ENST00000687119.1	n.179-30057G>T		intron_variant	Intron 2 of 3
ENSG00000289084	ENST00000687248.1	n.453+92115G>T		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.235 AC: 26174 AN: 111530 Hom.: 2419 Cov.: 23 AF XY: 0.224 AC XY: 7569 AN XY: 33762

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.300

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.235 AC: 26196 AN: 111585 Hom.: 2417 Cov.: 23 AF XY: 0.225 AC XY: 7600 AN XY: 33827

Gnomad4 AFR AF: 0.341

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.161

Gnomad4 EAS AF: 0.284

Gnomad4 SAS AF: 0.175

Gnomad4 FIN AF: 0.202

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.240

Alfa AF: 0.183 Hom.: 3737

Bravo AF: 0.239

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	14
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5925651; hg19: chrX-22669231;