10-84214480-T-C

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_033100.4(CDHR1):c.2439T>C(p.Thr813Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 1,608,950 control chromosomes in the GnomAD database, including 228,762 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.59 ( 27627 hom., cov: 33)

Exomes 𝑓: 0.52 ( 201135 hom. )

Consequence

CDHR1
NM_033100.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:9

Conservation

PhyloP100: -6.31

Publications

28 publications found

Variant links:

Genes affected

CDHR1 (HGNC:14550): (cadherin related family member 1) This gene belongs to the cadherin superfamily of calcium-dependent cell adhesion molecules. The encoded protein is a photoreceptor-specific cadherin that plays a role in outer segment disc morphogenesis. Mutations in this gene are associated with inherited retinal dystrophies. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2013]

CDHR1 Gene-Disease associations (from GenCC):

cone-rod dystrophy 15
Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics
cone-rod dystrophy
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
retinitis pigmentosa
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

CDHR1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BP6

Variant 10-84214480-T-C is Benign according to our data. Variant chr10-84214480-T-C is described in ClinVar as Benign. ClinVar VariationId is 194794.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.774 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDHR1	NM_033100.4 link	c.2439T>C	p.Thr813Thr	synonymous_variant	Exon 17 of 17	ENST00000623527.4	NP_149091.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDHR1	ENST00000623527.4 link	c.2439T>C	p.Thr813Thr	synonymous_variant	Exon 17 of 17	1	NM_033100.4	ENSP00000485478.1

Frequencies

GnomAD3 genomes

AF:

0.589

AC:

89508

AN:

151920

Hom.:

27574

Cov.:

show subpopulations

Gnomad AFR

AF:

0.781

Gnomad AMI

AF:

0.338

Gnomad AMR

AF:

0.583

Gnomad ASJ

AF:

0.571

Gnomad EAS

AF:

0.402

Gnomad SAS

AF:

0.477

Gnomad FIN

AF:

0.468

Gnomad MID

AF:

0.487

Gnomad NFE

AF:

0.520

Gnomad OTH

AF:

0.568

GnomAD2 exomes

AF:

0.532

AC:

131434

AN:

246990

AF XY:

0.524

show subpopulations

Gnomad AFR exome

AF:

0.784

Gnomad AMR exome

AF:

0.594

Gnomad ASJ exome

AF:

0.565

Gnomad EAS exome

AF:

0.393

Gnomad FIN exome

AF:

0.476

Gnomad NFE exome

AF:

0.524

Gnomad OTH exome

AF:

0.517

GnomAD4 exome

AF:

0.522

AC:

761089

AN:

1456910

Hom.:

201135

Cov.:

AF XY:

0.520

AC XY:

376714

AN XY:

725010

show subpopulations

African (AFR)

AF:

0.794

AC:

26544

AN:

33450

American (AMR)

AF:

0.593

AC:

26507

AN:

44694

Ashkenazi Jewish (ASJ)

AF:

0.569

AC:

14864

AN:

26108

East Asian (EAS)

AF:

0.355

AC:

14074

AN:

39692

South Asian (SAS)

AF:

0.469

AC:

40445

AN:

86254

European-Finnish (FIN)

AF:

0.480

AC:

23467

AN:

48850

Middle Eastern (MID)

AF:

0.501

AC:

2890

AN:

5766

European-Non Finnish (NFE)

AF:

0.522

AC:

580039

AN:

1111756

Other (OTH)

AF:

0.535

AC:

32259

AN:

60340

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.490

Heterozygous variant carriers

23815

47630

71444

95259

119074

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

16764

33528

50292

67056

83820

<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:

0.589

AC:

89624

AN:

152040

Hom.:

27627

Cov.:

AF XY:

0.584

AC XY:

43421

AN XY:

74306

show subpopulations

African (AFR)

AF:

0.782

AC:

32428

AN:

41492

American (AMR)

AF:

0.583

AC:

8907

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.571

AC:

1983

AN:

3472

East Asian (EAS)

AF:

0.402

AC:

2069

AN:

5142

South Asian (SAS)

AF:

0.477

AC:

2295

AN:

4814

European-Finnish (FIN)

AF:

0.468

AC:

4952

AN:

10570

Middle Eastern (MID)

AF:

0.497

AC:

146

AN:

294

European-Non Finnish (NFE)

AF:

0.520

AC:

35327

AN:

67952

Other (OTH)

AF:

0.572

AC:

1209

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1777

3554

5330

7107

8884

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

734

1468

2202

2936

3670

<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:

0.543

Hom.:

29146

Bravo

AF:

0.608

Asia WGS

AF:

0.496

AC:

1726

AN:

3478

EpiCase

AF:

0.517

EpiControl

AF:

0.524

ClinVar

Significance: Benign

Submissions summary: Benign:9

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:4

Nov 19, 2014

Eurofins Ntd Llc (ga)

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

- -

Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

- -

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not provided

Benign:3

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Apr 26, 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. -

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Cone-Rod Dystrophy, Recessive

Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Cone-rod dystrophy 15

Benign:1

Jul 14, 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

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.066

(source)

DANN

Benign

0.45

PhyloP100

-6.3

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

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over