Genetic Variant PTCHD1-AS:n.287+54827G>A (chrX-23215224-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000687248.2(PTCHD1-AS):n.287+54827G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 110,543 control chromosomes in the GnomAD database, including 3,264 homozygotes. There are 9,341 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 0.28 ( 3264 hom., 9341 hem., cov: 22)

Consequence

PTCHD1-AS
ENST00000687248.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0150

Publications

1 publications found

Variant links:

Genes affected

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

PTCHD1-AS links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.94).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.459 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTCHD1-AS	NR_073010.2 link	n.259+54827G>A		intron_variant	Intron 2 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTCHD1-AS	ENST00000687248.2 link	n.287+54827G>A		intron_variant	Intron 2 of 8

Frequencies

GnomAD3 genomes

AF:

0.285

AC:

31449

AN:

110487

Hom.:

3260

Cov.:

show subpopulations

Gnomad AFR

AF:

0.242

Gnomad AMI

AF:

0.307

Gnomad AMR

AF:

0.417

Gnomad ASJ

AF:

0.244

Gnomad EAS

AF:

0.478

Gnomad SAS

AF:

0.366

Gnomad FIN

AF:

0.251

Gnomad MID

AF:

0.253

Gnomad NFE

AF:

0.271

Gnomad OTH

AF:

0.311

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

GnomAD4 genome

AF:

0.285

AC:

31481

AN:

110543

Hom.:

3264

Cov.:

AF XY:

0.285

AC XY:

9341

AN XY:

32805

show subpopulations

African (AFR)

AF:

0.243

AC:

7386

AN:

30416

American (AMR)

AF:

0.418

AC:

4356

AN:

10425

Ashkenazi Jewish (ASJ)

AF:

0.244

AC:

643

AN:

2640

East Asian (EAS)

AF:

0.478

AC:

1645

AN:

3440

South Asian (SAS)

AF:

0.367

AC:

933

AN:

2545

European-Finnish (FIN)

AF:

0.251

AC:

1478

AN:

5892

Middle Eastern (MID)

AF:

0.254

AC:

AN:

213

European-Non Finnish (NFE)

AF:

0.271

AC:

14316

AN:

52795

Other (OTH)

AF:

0.308

AC:

464

AN:

1505

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

819

1638

2458

3277

4096

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

318

636

954

1272

1590

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.287

Hom.:

2138

Bravo

AF:

0.304

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.60

(source)

DANN

Benign

0.21

PhyloP100

0.015

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over