rs10487833

Variant names:

• chr7-105922199-T-G
• rs10487833
• ENST00000470188.5:n.818+9561T>G

Variant summary

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

The ENST00000470188.5(CDHR3):​n.818+9561T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 152,240 control chromosomes in the GnomAD database, including 1,504 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 0.13 (1504 hom., cov: 32)
• Consequence: CDHR3 ENST00000470188.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330
• 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.212 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+9561T>G		intron_variant	Intron 3 of 14	2
CDHR3	ENST00000472116.1	n.433-1424T>G		intron_variant	Intron 3 of 3	2
CDHR3	ENST00000488386.5	n.-16+44942T>G		intron_variant	Intron 1 of 3	3		ENSP00000419593.1

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19445 AN: 152122 Hom.: 1501 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.0958

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.0466

Gnomad SAS AF: 0.0654

Gnomad FIN AF: 0.0557

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.128 AC: 19464 AN: 152240 Hom.: 1504 Cov.: 32 AF XY: 0.122 AC XY: 9112 AN XY: 74428

African (AFR) AF: 0.215 AC: 8939 AN: 41508

American (AMR) AF: 0.0957 AC: 1464 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 522 AN: 3472

East Asian (EAS) AF: 0.0469 AC: 243 AN: 5186

South Asian (SAS) AF: 0.0650 AC: 313 AN: 4816

European-Finnish (FIN) AF: 0.0557 AC: 591 AN: 10614

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.102 AC: 6967 AN: 68024

Other (OTH) AF: 0.120 AC: 253 AN: 2116

Alfa AF: 0.114 Hom.: 1864

Bravo AF: 0.136

Asia WGS AF: 0.0640 AC: 224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.5
DANN	Benign	0.81
PhyloP100		-0.033

Splicing

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

Other links and lift over

dbSNP: rs10487833; hg19: chr7-105562645;