Variant 10-27413327-GC-GCC details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001034842.5(PTCHD3):c.923dupG(p.Ser309fs) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 1,613,714 control chromosomes in the GnomAD database, including 95,899 homozygotes. Variant has been reported in ClinVar as Benign (★). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: 𝑓 0.32 ( 8052 hom., cov: 0)

Exomes 𝑓: 0.34 ( 87847 hom. )

Consequence

PTCHD3
NM_001034842.5 frameshift

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.454

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 10-27413327-G-GC is Benign according to our data. Variant chr10-27413327-G-GC is described in ClinVar as [Benign]. Clinvar id is 403352.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTCHD3	NM_001034842.5 linkuse as main transcript	c.923dupG	p.Ser309fs	frameshift_variant	1/4		NP_001030014.2	Q3KNS1A0A8Q3VUI5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PTCHD3	ENST00000642324.1 linkuse as main transcript	c.923dupG	p.Ser309fs	frameshift_variant	1/4			ENSP00000495205.1

Frequencies

GnomAD3 genomes

AF:

0.320

AC:

48562

AN:

151816

Hom.:

8049

Cov.:

show subpopulations

Gnomad AFR

AF:

0.282

Gnomad AMI

AF:

0.427

Gnomad AMR

AF:

0.325

Gnomad ASJ

AF:

0.355

Gnomad EAS

AF:

0.163

Gnomad SAS

AF:

0.288

Gnomad FIN

AF:

0.294

Gnomad MID

AF:

0.296

Gnomad NFE

AF:

0.356

Gnomad OTH

AF:

0.344

GnomAD3 exomes

AF:

0.305

AC:

76766

AN:

251296

Hom.:

12547

AF XY:

0.310

AC XY:

42126

AN XY:

135840

show subpopulations

Gnomad AFR exome

AF:

0.280

Gnomad AMR exome

AF:

0.239

Gnomad ASJ exome

AF:

0.347

Gnomad EAS exome

AF:

0.158

Gnomad SAS exome

AF:

0.298

Gnomad FIN exome

AF:

0.294

Gnomad NFE exome

AF:

0.353

Gnomad OTH exome

AF:

0.315

GnomAD4 exome

AF:

0.341

AC:

497738

AN:

1461780

Hom.:

87847

Cov.:

AF XY:

0.340

AC XY:

246978

AN XY:

727194

show subpopulations

Gnomad4 AFR exome

AF:

0.278

Gnomad4 AMR exome

AF:

0.249

Gnomad4 ASJ exome

AF:

0.344

Gnomad4 EAS exome

AF:

0.130

Gnomad4 SAS exome

AF:

0.298

Gnomad4 FIN exome

AF:

0.300

Gnomad4 NFE exome

AF:

0.359

Gnomad4 OTH exome

AF:

0.336

GnomAD4 genome

AF:

0.320

AC:

48575

AN:

151934

Hom.:

8052

Cov.:

AF XY:

0.318

AC XY:

23602

AN XY:

74298

show subpopulations

Gnomad4 AFR

AF:

0.281

Gnomad4 AMR

AF:

0.325

Gnomad4 ASJ

AF:

0.355

Gnomad4 EAS

AF:

0.163

Gnomad4 SAS

AF:

0.288

Gnomad4 FIN

AF:

0.294

Gnomad4 NFE

AF:

0.356

Gnomad4 OTH

AF:

0.344

Bravo

AF:

0.315

Asia WGS

AF:

0.238

AC:

832

AN:

3478

EpiCase

AF:

0.360

EpiControl

AF:

0.363

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 28, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency in 1000Genomes: 584/2178=26.81% -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over