dbSNP rs2484173: PTCHD3:p.Ser511Ser (chr10-27399065-A-G) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The ENST00000642324.1(PTCHD3):c.1533T>C(p.Ser511Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.656 in 1,609,400 control chromosomes in the GnomAD database, including 353,605 homozygotes. 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 0.62 ( 29815 hom., cov: 30)

Exomes 𝑓: 0.66 ( 323790 hom. )

Consequence

PTCHD3
ENST00000642324.1 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.09

Publications

18 publications found

Variant links:

Genes affected

PTCHD3 (HGNC:24776): (patched domain containing 3 (gene/pseudogene)) Predicted to be located in sperm midpiece. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Apr 2022]

PTCHD3 links:

ENSG00000301548 (HGNC:):

ENSG00000301548 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP7

Synonymous conserved (PhyloP=-2.09 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.673 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTCHD3	NM_001034842.5 link	c.1533T>C	p.Ser511Ser	synonymous_variant	Exon 4 of 4		NP_001030014.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTCHD3	ENST00000642324.1 link	c.1533T>C	p.Ser511Ser	synonymous_variant	Exon 4 of 4			ENSP00000495205.1

Frequencies

GnomAD3 genomes

AF:

0.622

AC:

94262

AN:

151644

Hom.:

29785

Cov.:

show subpopulations

Gnomad AFR

AF:

0.548

Gnomad AMI

AF:

0.746

Gnomad AMR

AF:

0.562

Gnomad ASJ

AF:

0.749

Gnomad EAS

AF:

0.342

Gnomad SAS

AF:

0.664

Gnomad FIN

AF:

0.687

Gnomad MID

AF:

0.704

Gnomad NFE

AF:

0.678

Gnomad OTH

AF:

0.643

GnomAD2 exomes

AF:

0.615

AC:

154404

AN:

251090

AF XY:

0.631

show subpopulations

Gnomad AFR exome

AF:

0.545

Gnomad AMR exome

AF:

0.429

Gnomad ASJ exome

AF:

0.748

Gnomad EAS exome

AF:

0.350

Gnomad FIN exome

AF:

0.679

Gnomad NFE exome

AF:

0.677

Gnomad OTH exome

AF:

0.638

GnomAD4 exome

AF:

0.659

AC:

961123

AN:

1457638

Hom.:

323790

Cov.:

AF XY:

0.663

AC XY:

480822

AN XY:

725398

show subpopulations

African (AFR)

AF:

0.545

AC:

18193

AN:

33390

American (AMR)

AF:

0.447

AC:

19998

AN:

44708

Ashkenazi Jewish (ASJ)

AF:

0.747

AC:

19503

AN:

26106

East Asian (EAS)

AF:

0.275

AC:

10902

AN:

39680

South Asian (SAS)

AF:

0.697

AC:

60027

AN:

86166

European-Finnish (FIN)

AF:

0.682

AC:

36441

AN:

53412

Middle Eastern (MID)

AF:

0.739

AC:

4256

AN:

5762

European-Non Finnish (NFE)

AF:

0.679

AC:

752126

AN:

1108172

Other (OTH)

AF:

0.659

AC:

39677

AN:

60242

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.452

Heterozygous variant carriers

16144

32288

48432

64576

80720

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

19112

38224

57336

76448

95560

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.622

AC:

94345

AN:

151762

Hom.:

29815

Cov.:

AF XY:

0.623

AC XY:

46252

AN XY:

74184

show subpopulations

African (AFR)

AF:

0.549

AC:

22708

AN:

41358

American (AMR)

AF:

0.562

AC:

8569

AN:

15248

Ashkenazi Jewish (ASJ)

AF:

0.749

AC:

2597

AN:

3468

East Asian (EAS)

AF:

0.343

AC:

1769

AN:

5160

South Asian (SAS)

AF:

0.664

AC:

3193

AN:

4806

European-Finnish (FIN)

AF:

0.687

AC:

7231

AN:

10520

Middle Eastern (MID)

AF:

0.705

AC:

206

AN:

292

European-Non Finnish (NFE)

AF:

0.678

AC:

46041

AN:

67884

Other (OTH)

AF:

0.639

AC:

1351

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

1728

3457

5185

6914

8642

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

776

1552

2328

3104

3880

<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:

0.660

Hom.:

63384

Bravo

AF:

0.602

Asia WGS

AF:

0.506

AC:

1761

AN:

3478

EpiCase

AF:

0.691

EpiControl

AF:

0.695

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.57

(source)

DANN

Benign

0.54

PhyloP100

-2.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over