rs13438712

Positions:

• chr7-105902134-T-C

Variant summary

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

The ENST00000488386.5(CDHR3):​c.-16+24877T>C variant causes a intron, NMD transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 152,142 control chromosomes in the GnomAD database, including 7,835 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 0.31 (7835 hom., cov: 32)
• Consequence: CDHR3 ENST00000488386.5 intron, NMD_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350

Genes affected

CDHR3 (HGNC:26308): (cadherin related family member 3) Predicted to enable cadherin binding activity and calcium ion binding activity. Predicted to be involved in calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules; cell morphogenesis; and cell-cell junction organization. Located in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDHR3	ENST00000488386.5	c.-16+24877T>C		intron_variant, NMD_transcript_variant		3
CDHR3	ENST00000470188.5	n.438-8883T>C		intron_variant, non_coding_transcript_variant		2
CDHR3	ENST00000487084.1	n.463-8093T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46471 AN: 152024 Hom.: 7833 Cov.: 32

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.0427

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.306 AC: 46480 AN: 152142 Hom.: 7835 Cov.: 32 AF XY: 0.307 AC XY: 22854 AN XY: 74374

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.394

Gnomad4 EAS AF: 0.0430

Gnomad4 SAS AF: 0.365

Gnomad4 FIN AF: 0.391

Gnomad4 NFE AF: 0.368

Gnomad4 OTH AF: 0.330

Alfa AF: 0.357 Hom.: 19839

Bravo AF: 0.293

Asia WGS AF: 0.185 AC: 646 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.1
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13438712; hg19: chr7-105542580;