ENST00000687119.1:n.312+100539A>G

Variant names:

• chrX-22520385-T-C
• rs7876371
• ENST00000687119.1:n.312+100539A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000687119.1(PTCHD1-AS):​n.312+100539A>G variant causes a intron 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 ENST00000687119.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.76
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTCHD1-AS	NR_073010.2		n.454-130665A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTCHD1-AS	ENST00000687119.1		n.312+100539A>G		intron	N/A
	PTCHD1-AS	ENST00000687248.2		n.482-130665A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.228 AC: 25398 AN: 111370 Hom.: 2550 Cov.: 22

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

African (AFR) AF: 0.383 AC: 11702 AN: 30546

American (AMR) AF: 0.168 AC: 1768 AN: 10494

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 537 AN: 2644

East Asian (EAS) AF: 0.0476 AC: 169 AN: 3554

South Asian (SAS) AF: 0.215 AC: 577 AN: 2688

European-Finnish (FIN) AF: 0.120 AC: 729 AN: 6092

Middle Eastern (MID) AF: 0.173 AC: 37 AN: 214

European-Non Finnish (NFE) AF: 0.179 AC: 9467 AN: 53011

Other (OTH) AF: 0.234 AC: 350 AN: 1498

Alfa AF: 0.208 Hom.: 1214

Bravo AF: 0.241

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	15
DANN	Benign	0.85
PhyloP100		1.8
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs7876371; hg19: chrX-22538502;