rs13078807

chr3-85835000-A-G

Variant summary

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

The NM_001167675.2(CADM2):c.238+32804A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 151,694 control chromosomes in the GnomAD database, including 2,005 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 0.14 (2005 hom., cov: 32)
• Consequence: CADM2 NM_001167675.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.417

Genes affected

CADM2 (HGNC:29849): (cell adhesion molecule 2) This gene encodes a member of the synaptic cell adhesion molecule 1 (SynCAM) family which belongs to the immunoglobulin (Ig) superfamily. The encoded protein has three Ig-like domains and a cytosolic protein 4.1 binding site near the C-terminus. Proteins belonging to the protein 4.1 family crosslink spectrin and interact with other cytoskeletal proteins. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2012]

ACMG classification

Verdict is Benign. Variant got -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 = 0.197 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CADM2	NM_001167675.2	c.238+32804A>G		intron_variant		ENST00000383699.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CADM2	ENST00000383699.8	c.238+32804A>G		intron_variant		1	NM_001167675.2	A1
CADM2	ENST00000405615.2	c.217+32804A>G		intron_variant		1
CADM2	ENST00000407528.6	c.211+32804A>G		intron_variant		1		P4

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21858 AN: 151578 Hom.: 2008 Cov.: 32

Gnomad AFR AF: 0.0592

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.00464

Gnomad SAS AF: 0.0963

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.144 AC: 21846 AN: 151694 Hom.: 2005 Cov.: 32 AF XY: 0.139 AC XY: 10321 AN XY: 74146

Gnomad4 AFR AF: 0.0590

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.00465

Gnomad4 SAS AF: 0.0966

Gnomad4 FIN AF: 0.169

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.171

Alfa AF: 0.188 Hom.: 6109

Bravo AF: 0.138

Asia WGS AF: 0.0540 AC: 190 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	0.20
Dann	Benign	0.23

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs13078807; hg19: chr3-85884150;