rs17152355

Variant names:

• chr7-105934756-T-C
• rs17152355
• ENST00000470188.5:n.818+22118T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000470188.5(CDHR3):​n.818+22118T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 151,848 control chromosomes in the GnomAD database, including 2,449 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 0.18 (2449 hom., cov: 32)
• Consequence: CDHR3 ENST00000470188.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.223
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.25 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.818+22118T>C		intron_variant	Intron 3 of 14	2
CDHR3	ENST00000488386.5	n.-15-46212T>C		intron_variant	Intron 1 of 3	3		ENSP00000419593.1

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27055 AN: 151730 Hom.: 2439 Cov.: 32

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.178 AC: 27091 AN: 151848 Hom.: 2449 Cov.: 32 AF XY: 0.175 AC XY: 13001 AN XY: 74234

African (AFR) AF: 0.209 AC: 8621 AN: 41340

American (AMR) AF: 0.160 AC: 2442 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 604 AN: 3470

East Asian (EAS) AF: 0.261 AC: 1343 AN: 5142

South Asian (SAS) AF: 0.182 AC: 874 AN: 4796

European-Finnish (FIN) AF: 0.128 AC: 1352 AN: 10576

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.167 AC: 11333 AN: 67936

Other (OTH) AF: 0.175 AC: 370 AN: 2110

Alfa AF: 0.174 Hom.: 10417

Bravo AF: 0.184

Asia WGS AF: 0.225 AC: 783 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	2.6
DANN	Benign	0.71
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs17152355; hg19: chr7-105575202;