chr7-105902134-T-C

Variant names:

• chr7-105902134-T-C
• rs13438712
• ENST00000470188.5:n.438-8883T>C

Variant summary

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

The ENST00000470188.5(CDHR3):​n.438-8883T>C variant causes a intron 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 ENST00000470188.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350
• Publications: 6 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=-0.87).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDHR3	ENST00000470188.5	n.438-8883T>C		intron_variant	Intron 1 of 14	2
CDHR3	ENST00000487084.1	n.463-8093T>C		intron_variant	Intron 1 of 1	3
CDHR3	ENST00000488386.5	n.-16+24877T>C		intron_variant	Intron 1 of 3	3		ENSP00000419593.1

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

African (AFR) AF: 0.200 AC: 8321 AN: 41518

American (AMR) AF: 0.296 AC: 4530 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 1366 AN: 3470

East Asian (EAS) AF: 0.0430 AC: 223 AN: 5186

South Asian (SAS) AF: 0.365 AC: 1760 AN: 4820

European-Finnish (FIN) AF: 0.391 AC: 4132 AN: 10568

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.368 AC: 25017 AN: 67970

Other (OTH) AF: 0.330 AC: 698 AN: 2112

Alfa AF: 0.346 Hom.: 39695

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
PhyloP100		0.035

Splicing

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

Other links and lift over

dbSNP: rs13438712; hg19: chr7-105542580;