Variant rs3814212 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

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 links:

CDHR1 (HGNC:):

CDHR1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 id is 194795.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-84214625-A-G is described in Lovd as [Benign].

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/exons	MANE	Protein	UniProt
CDHR1	NM_033100.4 linkuse as main transcript	c.*4A>G		3_prime_UTR_variant	17/17	ENST00000623527.4	NP_149091.1	Q96JP9-1F1T0L2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDHR1	ENST00000623527.4 linkuse as main transcript	c.*4A>G		3_prime_UTR_variant	17/17	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

GnomAD3 exomes

AF:

0.586

AC:

139883

AN:

238670

Hom.:

42219

AF XY:

0.576

AC XY:

74904

AN XY:

130050

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 SAS exome

AF:

0.485

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

Gnomad4 AFR exome

AF:

0.886

Gnomad4 AMR exome

AF:

0.637

Gnomad4 ASJ exome

AF:

0.661

Gnomad4 EAS exome

AF:

0.355

Gnomad4 SAS exome

AF:

0.485

Gnomad4 FIN exome

AF:

0.556

Gnomad4 NFE exome

AF:

0.583

Gnomad4 OTH exome

AF:

0.600

GnomAD4 genome

AF:

0.660

AC:

100278

AN:

151996

Hom.:

34611

Cov.:

AF XY:

0.654

AC XY:

48598

AN XY:

74298

show subpopulations

Gnomad4 AFR

AF:

0.877

Gnomad4 AMR

AF:

0.644

Gnomad4 ASJ

AF:

0.669

Gnomad4 EAS

AF:

0.403

Gnomad4 SAS

AF:

0.495

Gnomad4 FIN

AF:

0.553

Gnomad4 NFE

AF:

0.582

Gnomad4 OTH

AF:

0.636

Alfa

AF:

0.607

Hom.:

29718

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

Benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Nov 19, 2014	- -
Benign, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Apr 26, 2018	- -

Cone-Rod Dystrophy, Recessive

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

4.7

DANN

Benign

0.38

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

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