rs7089142

Positions:

• chr10-84207180-A-G
• chr10-84207180-A-T

Variant summary

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

The ENST00000623527.4(CDHR1):​c.964-994A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.538 in 151,856 control chromosomes in the GnomAD database, including 23,326 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 0.54 (23326 hom., cov: 30)
• Consequence: CDHR1 ENST00000623527.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.33

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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDHR1	NM_033100.4	c.964-994A>G		intron_variant		ENST00000623527.4	NP_149091.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDHR1	ENST00000623527.4	c.964-994A>G		intron_variant		1	NM_033100.4	ENSP00000485478	P2
CDHR1	ENST00000332904.7	c.964-994A>G		intron_variant		1		ENSP00000331063	A2
CDHR1	ENST00000372117.6	c.344-994A>G		intron_variant		2		ENSP00000361189
CDHR1	ENST00000624091.1	c.*105-994A>G		intron_variant, NMD_transcript_variant		5		ENSP00000485460

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81601 AN: 151738 Hom.: 23277 Cov.: 30

Gnomad AFR AF: 0.739

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.516

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

GnomAD4 genome AF: 0.538 AC: 81719 AN: 151856 Hom.: 23326 Cov.: 30 AF XY: 0.532 AC XY: 39460 AN XY: 74220

Gnomad4 AFR AF: 0.739

Gnomad4 AMR AF: 0.505

Gnomad4 ASJ AF: 0.484

Gnomad4 EAS AF: 0.258

Gnomad4 SAS AF: 0.387

Gnomad4 FIN AF: 0.440

Gnomad4 NFE AF: 0.477

Gnomad4 OTH AF: 0.520

Alfa AF: 0.495 Hom.: 5945

Bravo AF: 0.554

Asia WGS AF: 0.396 AC: 1379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.025
DANN	Benign	0.38

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: rs7089142; hg19: chr10-85966936;