rs9852127

Variant names:

• chr3-85777586-G-A
• rs9852127
• NM_001167675.2:c.89-24461G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-85777586-G-A
• chr3-85777586-G-T

Variant summary

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

The NM_001167675.2(CADM2):​c.89-24461G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 152,072 control chromosomes in the GnomAD database, including 2,052 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 0.15 (2052 hom., cov: 32)
• Consequence: CADM2 NM_001167675.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.790
• 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=-0.91).
• 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 rank	MANE	Protein	UniProt
CADM2	NM_001167675.2	c.89-24461G>A		intron_variant	Intron 2 of 9	ENST00000383699.8	NP_001161147.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CADM2	ENST00000383699.8	c.89-24461G>A		intron_variant	Intron 2 of 9	1	NM_001167675.2	ENSP00000373200.3
CADM2	ENST00000405615.2	c.68-24461G>A		intron_variant	Intron 1 of 9	1		ENSP00000384193.2
CADM2	ENST00000407528.6	c.62-24461G>A		intron_variant	Intron 1 of 9	1		ENSP00000384575.2

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22508 AN: 151954 Hom.: 2055 Cov.: 32

Gnomad AFR AF: 0.0727

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.00463

Gnomad SAS AF: 0.0961

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.148 AC: 22495 AN: 152072 Hom.: 2052 Cov.: 32 AF XY: 0.143 AC XY: 10635 AN XY: 74326

African (AFR) AF: 0.0725 AC: 3008 AN: 41514

American (AMR) AF: 0.131 AC: 1996 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1067 AN: 3468

East Asian (EAS) AF: 0.00464 AC: 24 AN: 5174

South Asian (SAS) AF: 0.0959 AC: 462 AN: 4816

European-Finnish (FIN) AF: 0.169 AC: 1781 AN: 10556

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.200 AC: 13564 AN: 67970

Other (OTH) AF: 0.173 AC: 365 AN: 2114

Alfa AF: 0.187 Hom.: 2219

Bravo AF: 0.142

Asia WGS AF: 0.0570 AC: 200 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.099
DANN	Benign	0.30
PhyloP100		-0.79
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: rs9852127; hg19: chr3-85826736;