rs5926214

Variant names:

• chrX-22517291-G-A
• rs5926214
• ENST00000687119.1:n.312+103633C>T

Variant summary

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

The ENST00000687119.1(PTCHD1-AS):​n.312+103633C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 110,069 control chromosomes in the GnomAD database, including 4,997 homozygotes. There are 11,238 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 0.35 (4997 hom., 11238 hem., cov: 22)
• Consequence: PTCHD1-AS ENST00000687119.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.09
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTCHD1-AS	NR_073010.2	n.454-127571C>T		intron_variant	Intron 4 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTCHD1-AS	ENST00000687119.1	n.312+103633C>T		intron_variant	Intron 3 of 3
PTCHD1-AS	ENST00000687248.2	n.482-127571C>T		intron_variant	Intron 4 of 8

Frequencies

GnomAD3 genomes AF: 0.351 AC: 38572 AN: 110014 Hom.: 4998 Cov.: 22

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.432

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.351 AC: 38608 AN: 110069 Hom.: 4997 Cov.: 22 AF XY: 0.347 AC XY: 11238 AN XY: 32397

African (AFR) AF: 0.441 AC: 13277 AN: 30080

American (AMR) AF: 0.310 AC: 3191 AN: 10310

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1014 AN: 2641

East Asian (EAS) AF: 0.352 AC: 1234 AN: 3503

South Asian (SAS) AF: 0.509 AC: 1317 AN: 2586

European-Finnish (FIN) AF: 0.279 AC: 1620 AN: 5812

Middle Eastern (MID) AF: 0.421 AC: 90 AN: 214

European-Non Finnish (NFE) AF: 0.304 AC: 16011 AN: 52753

Other (OTH) AF: 0.385 AC: 577 AN: 1497

Alfa AF: 0.331 Hom.: 10939

Bravo AF: 0.355

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	7.9
DANN	Benign	0.74
PhyloP100		2.1

Splicing

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

Other links and lift over

dbSNP: rs5926214; hg19: chrX-22535408;