rs2727744

Variant names:

• chr7-105946500-C-T
• rs2727744
• ENST00000470188.5:n.819-28344C>T

Variant summary

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

The ENST00000470188.5(CDHR3):​n.819-28344C>T variant causes a intron 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 ENST00000470188.5 intron
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDHR3	ENST00000470188.5	n.819-28344C>T		intron_variant	Intron 3 of 14	2
CDHR3	ENST00000488386.5	n.-15-34468C>T		intron_variant	Intron 1 of 3	3		ENSP00000419593.1

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;