Genetic Variant PDZD7:c.928+20delC (chr10-101020597-TG-T) – ACMG Classification: Benign (-16 pts)

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_001195263.2(PDZD7):c.928+20delC variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.53 ( 22363 hom., cov: 0)

Exomes 𝑓: 0.49 ( 179328 hom. )

Consequence

PDZD7
NM_001195263.2 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -1.32

Variant links:

Genes affected

PDZD7 (HGNC:26257): (PDZ domain containing 7) This gene encodes a ciliary protein homologous to proteins which are mutated in Usher syndrome patients, and mutations and translocations involving this gene have been associated with two types of Usher syndrome. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2010]

PDZD7 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 10-101020597-TG-T is Benign according to our data. Variant chr10-101020597-TG-T is described in ClinVar as [Benign]. Clinvar id is 257618.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-101020597-TG-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PDZD7	NM_001195263.2 link	c.928+20delC		intron_variant	Intron 7 of 16	ENST00000619208.6	NP_001182192.1	Q9H5P4-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PDZD7	ENST00000619208.6 link	c.928+20delC		intron_variant	Intron 7 of 16	5	NM_001195263.2	ENSP00000480489.1		Q9H5P4-3

Frequencies

GnomAD3 genomes

AF:

0.534

AC:

80959

AN:

151668

Hom.:

22350

Cov.:

show subpopulations

Gnomad AFR

AF:

0.672

Gnomad AMI

AF:

0.496

Gnomad AMR

AF:

0.499

Gnomad ASJ

AF:

0.485

Gnomad EAS

AF:

0.234

Gnomad SAS

AF:

0.435

Gnomad FIN

AF:

0.436

Gnomad MID

AF:

0.604

Gnomad NFE

AF:

0.505

Gnomad OTH

AF:

0.529

GnomAD3 exomes

AF:

0.472

AC:

118222

AN:

250692

Hom.:

28847

AF XY:

0.471

AC XY:

63795

AN XY:

135462

show subpopulations

Gnomad AFR exome

AF:

0.670

Gnomad AMR exome

AF:

0.424

Gnomad ASJ exome

AF:

0.486

Gnomad EAS exome

AF:

0.226

Gnomad SAS exome

AF:

0.444

Gnomad FIN exome

AF:

0.449

Gnomad NFE exome

AF:

0.507

Gnomad OTH exome

AF:

0.493

GnomAD4 exome

AF:

0.493

AC:

716318

AN:

1454146

Hom.:

179328

Cov.:

AF XY:

0.491

AC XY:

355202

AN XY:

724000

show subpopulations

Gnomad4 AFR exome

AF:

0.680

Gnomad4 AMR exome

AF:

0.436

Gnomad4 ASJ exome

AF:

0.487

Gnomad4 EAS exome

AF:

0.243

Gnomad4 SAS exome

AF:

0.447

Gnomad4 FIN exome

AF:

0.450

Gnomad4 NFE exome

AF:

0.504

Gnomad4 OTH exome

AF:

0.490

GnomAD4 genome

AF:

0.534

AC:

81006

AN:

151788

Hom.:

22363

Cov.:

AF XY:

0.528

AC XY:

39143

AN XY:

74170

show subpopulations

Gnomad4 AFR

AF:

0.672

Gnomad4 AMR

AF:

0.498

Gnomad4 ASJ

AF:

0.485

Gnomad4 EAS

AF:

0.234

Gnomad4 SAS

AF:

0.434

Gnomad4 FIN

AF:

0.436

Gnomad4 NFE

AF:

0.505

Gnomad4 OTH

AF:

0.526

Alfa

AF:

0.519

Hom.:

3730

Bravo

AF:

0.544

Asia WGS

AF:

0.350

AC:

1222

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jun 14, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

not specified

Benign:1

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Usher syndrome type 2C

Benign:1

Sep 05, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Hearing loss, autosomal recessive 57

Benign:1

Sep 05, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

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.

10-101020597-TGG-TG

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