NM_033100.4:c.*4A>G

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.*4A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.589 in 1,599,184 control chromosomes in the GnomAD database, including 282,673 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.66 ( 34611 hom., cov: 31)

Exomes 𝑓: 0.58 ( 248062 hom. )

Consequence

CDHR1
NM_033100.4 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:7

Conservation

PhyloP100: 0.160

Publications

19 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=-0.85).

BP6

Variant 10-84214625-A-G is Benign according to our data. Variant chr10-84214625-A-G is described in ClinVar as Benign. ClinVar VariationId is 194795.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDHR1	NM_033100.4 link	c.*4A>G		3_prime_UTR_variant	Exon 17 of 17	ENST00000623527.4	NP_149091.1	Q96JP9-1F1T0L2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDHR1	ENST00000623527.4 link	c.*4A>G		3_prime_UTR_variant	Exon 17 of 17	1	NM_033100.4	ENSP00000485478.1		Q96JP9-1

Frequencies

GnomAD3 genomes

AF:

0.659

AC:

100153

AN:

151878

Hom.:

34548

Cov.:

show subpopulations

Gnomad AFR

AF:

0.877

Gnomad AMI

AF:

0.383

Gnomad AMR

AF:

0.645

Gnomad ASJ

AF:

0.669

Gnomad EAS

AF:

0.403

Gnomad SAS

AF:

0.495

Gnomad FIN

AF:

0.553

Gnomad MID

AF:

0.614

Gnomad NFE

AF:

0.582

Gnomad OTH

AF:

0.633

GnomAD2 exomes

AF:

0.586

AC:

139883

AN:

238670

AF XY:

0.576

show subpopulations

Gnomad AFR exome

AF:

0.881

Gnomad AMR exome

AF:

0.636

Gnomad ASJ exome

AF:

0.655

Gnomad EAS exome

AF:

0.393

Gnomad FIN exome

AF:

0.552

Gnomad NFE exome

AF:

0.586

Gnomad OTH exome

AF:

0.590

GnomAD4 exome

AF:

0.581

AC:

841118

AN:

1447188

Hom.:

248062

Cov.:

AF XY:

0.577

AC XY:

415643

AN XY:

720308

show subpopulations

African (AFR)

AF:

0.886

AC:

29674

AN:

33474

American (AMR)

AF:

0.637

AC:

28479

AN:

44700

Ashkenazi Jewish (ASJ)

AF:

0.661

AC:

17283

AN:

26128

East Asian (EAS)

AF:

0.355

AC:

14103

AN:

39696

South Asian (SAS)

AF:

0.485

AC:

41817

AN:

86232

European-Finnish (FIN)

AF:

0.556

AC:

21762

AN:

39156

Middle Eastern (MID)

AF:

0.583

AC:

3361

AN:

5766

European-Non Finnish (NFE)

AF:

0.583

AC:

648483

AN:

1111736

Other (OTH)

AF:

0.600

AC:

36156

AN:

60300

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.480

Heterozygous variant carriers

18525

37050

55574

74099

92624

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

17916

35832

53748

71664

89580

<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:

0.660

AC:

100278

AN:

151996

Hom.:

34611

Cov.:

AF XY:

0.654

AC XY:

48598

AN XY:

74298

show subpopulations

African (AFR)

AF:

0.877

AC:

36396

AN:

41480

American (AMR)

AF:

0.644

AC:

9847

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.669

AC:

2323

AN:

3472

East Asian (EAS)

AF:

0.403

AC:

2061

AN:

5120

South Asian (SAS)

AF:

0.495

AC:

2379

AN:

4808

European-Finnish (FIN)

AF:

0.553

AC:

5843

AN:

10562

Middle Eastern (MID)

AF:

0.629

AC:

185

AN:

294

European-Non Finnish (NFE)

AF:

0.582

AC:

39554

AN:

67958

Other (OTH)

AF:

0.636

AC:

1341

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1617

3235

4852

6470

8087

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:

0.618

Hom.:

40174

Bravo

AF:

0.678

Asia WGS

AF:

0.513

AC:

1786

AN:

3478

EpiCase

AF:

0.580

EpiControl

AF:

0.585

ClinVar

Significance: Benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:4

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

- -

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

- -

Nov 19, 2014

Eurofins Ntd Llc (ga)

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not provided

Benign:2

Apr 26, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

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

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

4.7

(source)

DANN

Benign

0.38

PhyloP100

0.16

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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