rs7876371

chrX-22520385-T-C

Variant summary

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

The NR_073010.2(PTCHD1-AS):n.454-130665A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 111,422 control chromosomes in the GnomAD database, including 2,551 homozygotes. There are 7,117 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 (2551 hom., 7117 hem., cov: 22)
• Consequence: PTCHD1-AS NR_073010.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.76

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTCHD1-AS	NR_073010.2	n.454-130665A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000687248.1	n.454-130665A>G		intron_variant, non_coding_transcript_variant
	ENST00000687119.1	n.312+100539A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.228 AC: 25398 AN: 111370 Hom.: 2550 Cov.: 22 AF XY: 0.211 AC XY: 7092 AN XY: 33618

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.0474

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.183

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.228 AC: 25427 AN: 111422 Hom.: 2551 Cov.: 22 AF XY: 0.211 AC XY: 7117 AN XY: 33680

Gnomad4 AFR AF: 0.383

Gnomad4 AMR AF: 0.168

Gnomad4 ASJ AF: 0.203

Gnomad4 EAS AF: 0.0476

Gnomad4 SAS AF: 0.215

Gnomad4 FIN AF: 0.120

Gnomad4 NFE AF: 0.179

Gnomad4 OTH AF: 0.234

Alfa AF: 0.208 Hom.: 1214

Bravo AF: 0.241

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
Cadd	Benign	15
Dann	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7876371; hg19: chrX-22538502;