X-23082228-C-T

Variant names:

• chrX-23082228-C-T
• rs16982419
• ENST00000687248.2:n.288-18107G>A

Variant summary

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

The NR_073010.2(PTCHD1-AS):​n.260-18107G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 110,436 control chromosomes in the GnomAD database, including 6,946 homozygotes. There are 12,359 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 0.39 (6946 hom., 12359 hem., cov: 22)
• Consequence: PTCHD1-AS NR_073010.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162
• 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.597 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_073010.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTCHD1-AS	NR_073010.2		n.260-18107G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTCHD1-AS	ENST00000687248.2		n.288-18107G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.391 AC: 43179 AN: 110380 Hom.: 6947 Cov.: 22

Gnomad AFR AF: 0.605

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.391 AC: 43211 AN: 110436 Hom.: 6946 Cov.: 22 AF XY: 0.377 AC XY: 12359 AN XY: 32750

African (AFR) AF: 0.605 AC: 18328 AN: 30312

American (AMR) AF: 0.348 AC: 3617 AN: 10391

Ashkenazi Jewish (ASJ) AF: 0.346 AC: 909 AN: 2628

East Asian (EAS) AF: 0.456 AC: 1575 AN: 3456

South Asian (SAS) AF: 0.353 AC: 917 AN: 2595

European-Finnish (FIN) AF: 0.351 AC: 2050 AN: 5848

Middle Eastern (MID) AF: 0.393 AC: 84 AN: 214

European-Non Finnish (NFE) AF: 0.283 AC: 14969 AN: 52834

Other (OTH) AF: 0.361 AC: 540 AN: 1494

Alfa AF: 0.366 Hom.: 2593

Bravo AF: 0.406

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.81
DANN	Benign	0.25
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs16982419; hg19: chrX-23100345;