Genetic Variant PTCHD1-AS:n.178+70093T>C (chrX-22873960-A-G) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000687119.1(PTCHD1-AS):n.178+70093T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.74 ( 21638 hom., 23591 hem., cov: 22)

Failed GnomAD Quality Control

Consequence

PTCHD1-AS
ENST00000687119.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.317

Publications

6 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: Likely_benign. The variant received -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTCHD1-AS	NR_073010.2 link	n.344-130622T>C		intron_variant	Intron 3 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTCHD1-AS	ENST00000687119.1 link	n.178+70093T>C		intron_variant	Intron 2 of 3
PTCHD1-AS	ENST00000687248.2 link	n.372-130622T>C		intron_variant	Intron 3 of 8

Frequencies

GnomAD3 genomes

AF:

0.743

AC:

81133

AN:

109184

Hom.:

21637

Cov.:

show subpopulations

Gnomad AFR

AF:

0.837

Gnomad AMI

AF:

0.797

Gnomad AMR

AF:

0.782

Gnomad ASJ

AF:

0.741

Gnomad EAS

AF:

0.868

Gnomad SAS

AF:

0.874

Gnomad FIN

AF:

0.661

Gnomad MID

AF:

0.795

Gnomad NFE

AF:

0.675

Gnomad OTH

AF:

0.741

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

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.743

AC:

81189

AN:

109232

Hom.:

21638

Cov.:

AF XY:

0.746

AC XY:

23591

AN XY:

31638

show subpopulations

African (AFR)

AF:

0.838

AC:

25234

AN:

30119

American (AMR)

AF:

0.782

AC:

7947

AN:

10162

Ashkenazi Jewish (ASJ)

AF:

0.741

AC:

1947

AN:

2626

East Asian (EAS)

AF:

0.868

AC:

2944

AN:

3393

South Asian (SAS)

AF:

0.873

AC:

2252

AN:

2579

European-Finnish (FIN)

AF:

0.661

AC:

3666

AN:

5548

Middle Eastern (MID)

AF:

0.785

AC:

164

AN:

209

European-Non Finnish (NFE)

AF:

0.675

AC:

35385

AN:

52426

Other (OTH)

AF:

0.744

AC:

1115

AN:

1499

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

738

1476

2213

2951

3689

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

690

1380

2070

2760

3450

<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:

0.708

Hom.:

25987

Bravo

AF:

0.753

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

4.7

(source)

DANN

Benign

0.83

PhyloP100

0.32

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