rs2727744

chr7-105946500-C-T

Variant summary

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

The ENST00000488386.5(CDHR3):c.-15-34468C>T variant causes a intron, NMD transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.622 in 152,028 control chromosomes in the GnomAD database, including 30,104 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 0.62 (30104 hom., cov: 32)
• Consequence: CDHR3 ENST00000488386.5 intron, NMD_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.688

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=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.725 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.-15-34468C>T		intron_variant, NMD_transcript_variant		3
CDHR3	ENST00000470188.5	n.819-28344C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.622 AC: 94533 AN: 151912 Hom.: 30065 Cov.: 32

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.681

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.726

Gnomad SAS AF: 0.744

Gnomad FIN AF: 0.654

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.622 AC: 94628 AN: 152028 Hom.: 30104 Cov.: 32 AF XY: 0.625 AC XY: 46477 AN XY: 74322

Gnomad4 AFR AF: 0.476

Gnomad4 AMR AF: 0.682

Gnomad4 ASJ AF: 0.586

Gnomad4 EAS AF: 0.726

Gnomad4 SAS AF: 0.745

Gnomad4 FIN AF: 0.654

Gnomad4 NFE AF: 0.680

Gnomad4 OTH AF: 0.616

Alfa AF: 0.666 Hom.: 60215

Bravo AF: 0.615

Asia WGS AF: 0.713 AC: 2481 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	0.72
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2727744; hg19: chr7-105586946;