rs6549011

Positions:

• chr3-85047341-A-G
• chr3-85047341-A-T

Variant summary

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

The NM_001167675.2(CADM2):​c.61+87673A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.595 in 151,878 control chromosomes in the GnomAD database, including 27,777 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 0.60 (27777 hom., cov: 31)
• Consequence: CADM2 NM_001167675.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.342

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]

LOC124906200 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.64 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CADM2	NM_001167675.2	c.61+87673A>G		intron_variant		ENST00000383699.8	NP_001161147.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CADM2	ENST00000383699.8	c.61+87673A>G		intron_variant		1	NM_001167675.2	ENSP00000373200.3
CADM2	ENST00000407528.6	c.61+87673A>G		intron_variant		1		ENSP00000384575.2

Frequencies

GnomAD3 genomes AF: 0.595 AC: 90373 AN: 151760 Hom.: 27766 Cov.: 31

Gnomad AFR AF: 0.614

Gnomad AMI AF: 0.902

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.672

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.503

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.595 AC: 90421 AN: 151878 Hom.: 27777 Cov.: 31 AF XY: 0.586 AC XY: 43509 AN XY: 74202

Gnomad4 AFR AF: 0.614

Gnomad4 AMR AF: 0.493

Gnomad4 ASJ AF: 0.672

Gnomad4 EAS AF: 0.227

Gnomad4 SAS AF: 0.503

Gnomad4 FIN AF: 0.513

Gnomad4 NFE AF: 0.645

Gnomad4 OTH AF: 0.609

Alfa AF: 0.632 Hom.: 29067

Bravo AF: 0.593

Asia WGS AF: 0.351 AC: 1225 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6549011; hg19: chr3-85096492;