ENST00000687119.1:n.83-20194A>G

Variant names:

• chrX-22964342-T-C
• rs4618863
• ENST00000687119.1:n.83-20194A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000687119.1(PTCHD1-AS):​n.83-20194A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 111,231 control chromosomes in the GnomAD database, including 1,871 homozygotes. There are 7,012 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 0.21 (1871 hom., 7012 hem., cov: 23)
• Consequence: PTCHD1-AS ENST00000687119.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.133
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.356 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTCHD1-AS	NR_073010.2	n.343+99696A>G		intron_variant	Intron 3 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTCHD1-AS	ENST00000687119.1	n.83-20194A>G		intron_variant	Intron 1 of 3
PTCHD1-AS	ENST00000687248.2	n.371+99696A>G		intron_variant	Intron 3 of 8

Frequencies

GnomAD3 genomes AF: 0.211 AC: 23445 AN: 111175 Hom.: 1863 Cov.: 23

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.246

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.211 AC: 23469 AN: 111231 Hom.: 1871 Cov.: 23 AF XY: 0.209 AC XY: 7012 AN XY: 33499

African (AFR) AF: 0.167 AC: 5118 AN: 30673

American (AMR) AF: 0.275 AC: 2875 AN: 10462

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 655 AN: 2641

East Asian (EAS) AF: 0.372 AC: 1301 AN: 3493

South Asian (SAS) AF: 0.304 AC: 805 AN: 2652

European-Finnish (FIN) AF: 0.214 AC: 1267 AN: 5925

Middle Eastern (MID) AF: 0.251 AC: 54 AN: 215

European-Non Finnish (NFE) AF: 0.206 AC: 10927 AN: 52968

Other (OTH) AF: 0.225 AC: 342 AN: 1522

Alfa AF: 0.213 Hom.: 17255

Bravo AF: 0.216

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.1
DANN	Benign	0.70
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs4618863; hg19: chrX-22982459;