Variant 10-27399172-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM4BP6_ModerateBS2

The NM_001034842.5(PTCHD3):c.1426C>T(p.Arg476Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00683 in 1,607,094 control chromosomes in the GnomAD database, including 66 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0044 ( 2 hom., cov: 30)

Exomes 𝑓: 0.0071 ( 64 hom. )

Consequence

PTCHD3
NM_001034842.5 stop_gained

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.765

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 Likely_benign. Variant got -4 ACMG points.

PM4

Stoplost variant in NM_001034842.5 Downstream stopcodon found after 34 codons.

BP6

Variant 10-27399172-G-A is Benign according to our data. Variant chr10-27399172-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2640379.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr10-27399172-G-A is described in Lovd as [Benign].

BS2

High Homozygotes in GnomAd at 2 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTCHD3	NM_001034842.5 linkuse as main transcript	c.1426C>T	p.Arg476Ter	stop_gained	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTCHD3	ENST00000642324.1 linkuse as main transcript	c.1426C>T	p.Arg476Ter	stop_gained	4/4			P1

Frequencies

GnomAD3 genomes

AF:

0.00441

AC:

658

AN:

149374

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00133

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.00101

Gnomad ASJ

AF:

0.00116

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00170

Gnomad FIN

AF:

0.00338

Gnomad MID

AF:

0.00327

Gnomad NFE

AF:

0.00787

Gnomad OTH

AF:

0.00490

GnomAD3 exomes

AF:

0.00522

AC:

1285

AN:

246286

Hom.:

AF XY:

0.00520

AC XY:

695

AN XY:

133646

show subpopulations

Gnomad AFR exome

AF:

0.00148

Gnomad AMR exome

AF:

0.000897

Gnomad ASJ exome

AF:

0.00159

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00180

Gnomad FIN exome

AF:

0.00405

Gnomad NFE exome

AF:

0.00938

Gnomad OTH exome

AF:

0.00479

GnomAD4 exome

AF:

0.00708

AC:

10316

AN:

1457624

Hom.:

Cov.:

AF XY:

0.00679

AC XY:

4924

AN XY:

725368

show subpopulations

Gnomad4 AFR exome

AF:

0.00105

Gnomad4 AMR exome

AF:

0.00103

Gnomad4 ASJ exome

AF:

0.00191

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00186

Gnomad4 FIN exome

AF:

0.00539

Gnomad4 NFE exome

AF:

0.00851

Gnomad4 OTH exome

AF:

0.00479

GnomAD4 genome

AF:

0.00440

AC:

657

AN:

149470

Hom.:

Cov.:

AF XY:

0.00388

AC XY:

282

AN XY:

72642

show subpopulations

Gnomad4 AFR

AF:

0.00133

Gnomad4 AMR

AF:

0.00101

Gnomad4 ASJ

AF:

0.00116

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00171

Gnomad4 FIN

AF:

0.00338

Gnomad4 NFE

AF:

0.00785

Gnomad4 OTH

AF:

0.00485

Alfa

AF:

0.00693

Hom.:

Bravo

AF:

0.00438

TwinsUK

AF:

0.00971

AC:

ALSPAC

AF:

0.00804

AC:

ESP6500AA

AF:

0.00113

AC:

ESP6500EA

AF:

0.00860

AC:

ExAC

AF:

0.00604

AC:

733

Asia WGS

AF:

0.000577

AC:

AN:

3478

EpiCase

AF:

0.00638

EpiControl

AF:

0.00670

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Mar 01, 2022

PTCHD3: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.0085

BayesDel_noAF

Pathogenic

0.23

Cadd

Pathogenic

Dann

Benign

0.95

Eigen

Benign

-0.12

Eigen_PC

Benign

-0.52

FATHMM_MKL

Benign

0.026

MutationTaster

Benign

1.0

Vest4

0.20

GERP RS

-1.7

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