rs13323436

Variant names:

• chr3-85453695-T-A
• rs13323436
• NM_001167675.2:c.62-272827T>A

Your query was ambiguous. Multiple possible variants found:

• chr3-85453695-T-A
• chr3-85453695-T-C

Variant summary

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

The NM_001167675.2(CADM2):​c.62-272827T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0556 in 152,184 control chromosomes in the GnomAD database, including 359 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 0.056 (359 hom., cov: 32)
• Consequence: CADM2 NM_001167675.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.386
• Publications: 8 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0787 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CADM2	NM_001167675.2	c.62-272827T>A		intron_variant	Intron 1 of 9	ENST00000383699.8	NP_001161147.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CADM2	ENST00000383699.8	c.62-272827T>A		intron_variant	Intron 1 of 9	1	NM_001167675.2	ENSP00000373200.3
CADM2	ENST00000407528.6	c.62-348352T>A		intron_variant	Intron 1 of 9	1		ENSP00000384575.2

Frequencies

GnomAD3 genomes AF: 0.0557 AC: 8472 AN: 152066 Hom.: 360 Cov.: 32

Gnomad AFR AF: 0.0153

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.0472

Gnomad ASJ AF: 0.0550

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0209

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0805

Gnomad OTH AF: 0.0609

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

GnomAD4 genome AF: 0.0556 AC: 8464 AN: 152184 Hom.: 359 Cov.: 32 AF XY: 0.0542 AC XY: 4032 AN XY: 74400

African (AFR) AF: 0.0152 AC: 633 AN: 41570

American (AMR) AF: 0.0471 AC: 719 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0550 AC: 191 AN: 3470

East Asian (EAS) AF: 0.000580 AC: 3 AN: 5176

South Asian (SAS) AF: 0.0207 AC: 100 AN: 4826

European-Finnish (FIN) AF: 0.103 AC: 1090 AN: 10578

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0805 AC: 5472 AN: 67980

Other (OTH) AF: 0.0593 AC: 125 AN: 2108

Alfa AF: 0.0359 Hom.: 31

Bravo AF: 0.0508

Asia WGS AF: 0.0110 AC: 39 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.70
PhyloP100		-0.39
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs13323436; hg19: chr3-85502845; COSMIC: COSV67378993;