rs10487833

chr7-105922199-T-G

Variant summary

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

The ENST00000488386.5(CDHR3):c.-16+44942T>G variant causes a intron, NMD transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 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 ENST00000488386.5 intron, NMD_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330

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=-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDHR3	ENST00000488386.5	c.-16+44942T>G		intron_variant, NMD_transcript_variant		3
CDHR3	ENST00000470188.5	n.818+9561T>G		intron_variant, non_coding_transcript_variant		2
CDHR3	ENST00000472116.1	n.433-1424T>G		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.215

Gnomad4 AMR AF: 0.0957

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.0469

Gnomad4 SAS AF: 0.0650

Gnomad4 FIN AF: 0.0557

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.120

Alfa AF: 0.111 Hom.: 1413

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10487833; hg19: chr7-105562645;