dbSNP rs79239487: CDHR1:c.297+6G>A (chr10-84196656-G-A) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_033100.4(CDHR1):c.297+6G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00664 in 1,614,182 control chromosomes in the GnomAD database, including 401 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0099 ( 46 hom., cov: 32)

Exomes 𝑓: 0.0063 ( 355 hom. )

Consequence

CDHR1
NM_033100.4 splice_region, intron

Scores

Splicing: ADA: 0.0005256

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.0330

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:

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=-0.75).

BP6

Variant 10-84196656-G-A is Benign according to our data. Variant chr10-84196656-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 262214.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.117 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDHR1	NM_033100.4 link	c.297+6G>A		splice_region_variant, intron_variant	Intron 3 of 16	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.297+6G>A		splice_region_variant, intron_variant	Intron 3 of 16	1	NM_033100.4	ENSP00000485478.1		Q96JP9-1
CDHR1	ENST00000332904.7 link	c.297+6G>A		splice_region_variant, intron_variant	Intron 3 of 16	1		ENSP00000331063.3		Q96JP9-2

Frequencies

GnomAD3 genomes

AF:

0.00995

AC:

1514

AN:

152194

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0134

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00157

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.125

Gnomad SAS

AF:

0.0369

Gnomad FIN

AF:

0.00461

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000559

Gnomad OTH

AF:

0.00956

GnomAD3 exomes

AF:

0.0148

AC:

3733

AN:

251482

Hom.:

163

AF XY:

0.0154

AC XY:

2090

AN XY:

135918

show subpopulations

Gnomad AFR exome

AF:

0.0137

Gnomad AMR exome

AF:

0.000607

Gnomad ASJ exome

AF:

0.0000992

Gnomad EAS exome

AF:

0.123

Gnomad SAS exome

AF:

0.0326

Gnomad FIN exome

AF:

0.00573

Gnomad NFE exome

AF:

0.000659

Gnomad OTH exome

AF:

0.00619

GnomAD4 exome

AF:

0.00630

AC:

9210

AN:

1461870

Hom.:

355

Cov.:

AF XY:

0.00721

AC XY:

5245

AN XY:

727244

show subpopulations

Gnomad4 AFR exome

AF:

0.0145

Gnomad4 AMR exome

AF:

0.000604

Gnomad4 ASJ exome

AF:

0.000115

Gnomad4 EAS exome

AF:

0.109

Gnomad4 SAS exome

AF:

0.0336

Gnomad4 FIN exome

AF:

0.00528

Gnomad4 NFE exome

AF:

0.000490

Gnomad4 OTH exome

AF:

0.00997

GnomAD4 genome

AF:

0.00994

AC:

1514

AN:

152312

Hom.:

Cov.:

AF XY:

0.0112

AC XY:

835

AN XY:

74488

show subpopulations

Gnomad4 AFR

AF:

0.0134

Gnomad4 AMR

AF:

0.00157

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.125

Gnomad4 SAS

AF:

0.0367

Gnomad4 FIN

AF:

0.00461

Gnomad4 NFE

AF:

0.000559

Gnomad4 OTH

AF:

0.00993

Alfa

AF:

0.00229

Hom.:

Bravo

AF:

0.0104

Asia WGS

AF:

0.0680

AC:

235

AN:

3478

EpiCase

AF:

0.000545

EpiControl

AF:

0.000237

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jan 23, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified

Benign:1

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Cone-Rod Dystrophy, Recessive

Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Likely 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

-0.75

CADD

Benign

5.3

DANN

Benign

0.61

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.00053

dbscSNV1_RF

Benign

0.042

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