rs9812103

Variant names:

• chr3-85937570-A-C
• rs9812103
• NM_001167675.2:c.791+1713A>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.791+1713A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 151,770 control chromosomes in the GnomAD database, including 4,039 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 0.22 (4039 hom., cov: 32)
• Consequence: CADM2 NM_001167675.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.57
• Publications: 7 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=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001167675.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CADM2	NM_001167675.2	MANE Select	c.791+1713A>C		intron	N/A	NP_001161147.1	Q8N3J6-2
	CADM2	NM_001375960.1		c.791+1713A>C		intron	N/A	NP_001362889.1
	CADM2	NM_153184.4		c.770+1713A>C		intron	N/A	NP_694854.2	Q8N3J6-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CADM2	ENST00000383699.8	TSL:1 MANE Select	c.791+1713A>C		intron	N/A	ENSP00000373200.3	Q8N3J6-2
	CADM2	ENST00000405615.2	TSL:1	c.770+1713A>C		intron	N/A	ENSP00000384193.2	Q8N3J6-3
	CADM2	ENST00000407528.6	TSL:1	c.764+1713A>C		intron	N/A	ENSP00000384575.2	Q8N3J6-1

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32880 AN: 151652 Hom.: 4036 Cov.: 32

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.140

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.217 AC: 32898 AN: 151770 Hom.: 4039 Cov.: 32 AF XY: 0.215 AC XY: 15981 AN XY: 74170

African (AFR) AF: 0.337 AC: 13978 AN: 41428

American (AMR) AF: 0.206 AC: 3130 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 729 AN: 3466

East Asian (EAS) AF: 0.134 AC: 693 AN: 5158

South Asian (SAS) AF: 0.163 AC: 783 AN: 4818

European-Finnish (FIN) AF: 0.156 AC: 1653 AN: 10574

Middle Eastern (MID) AF: 0.144 AC: 42 AN: 292

European-Non Finnish (NFE) AF: 0.167 AC: 11296 AN: 67814

Other (OTH) AF: 0.211 AC: 444 AN: 2106

Alfa AF: 0.178 Hom.: 11032

Bravo AF: 0.224

Asia WGS AF: 0.150 AC: 522 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	9.4
DANN	Benign	0.87
PhyloP100		1.6
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9812103; hg19: chr3-85986720;