rs10788333

Positions:

• chr10-84200393-C-A
• chr10-84200393-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_033100.4(CDHR1):​c.439-208C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.518 in 151,840 control chromosomes in the GnomAD database, including 21,159 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.52 (21159 hom., cov: 31)
• Consequence: CDHR1 NM_033100.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.42

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.673 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDHR1	NM_033100.4	c.439-208C>A		intron_variant		ENST00000623527.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDHR1	ENST00000623527.4	c.439-208C>A		intron_variant		1	NM_033100.4	P2
CDHR1	ENST00000332904.7	c.439-208C>A		intron_variant		1		A2

Frequencies

GnomAD3 genomes AF: 0.518 AC: 78562 AN: 151720 Hom.: 21111 Cov.: 31

Gnomad AFR AF: 0.680

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.503

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.518 AC: 78675 AN: 151840 Hom.: 21159 Cov.: 31 AF XY: 0.516 AC XY: 38298 AN XY: 74230

Gnomad4 AFR AF: 0.680

Gnomad4 AMR AF: 0.526

Gnomad4 ASJ AF: 0.473

Gnomad4 EAS AF: 0.390

Gnomad4 SAS AF: 0.440

Gnomad4 FIN AF: 0.443

Gnomad4 NFE AF: 0.451

Gnomad4 OTH AF: 0.508

Alfa AF: 0.452 Hom.: 14436

Bravo AF: 0.534

Asia WGS AF: 0.471 AC: 1641 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.085
DANN	Benign	0.37

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

Other links and lift over

dbSNP: rs10788333; hg19: chr10-85960149;