rs11215406

chr11-115194362-T-C

Variant summary

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

The NM_001301043.2(CADM1):c.1112-3421A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 152,190 control chromosomes in the GnomAD database, including 3,595 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 0.20 (3595 hom., cov: 33)
• Consequence: CADM1 NM_001301043.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.293

Genes affected

CADM1 (HGNC:5951): (cell adhesion molecule 1) Enables signaling receptor binding activity. Involved in several processes, including cell recognition; positive regulation of cytokine production; and susceptibility to natural killer cell mediated cytotoxicity. Located in plasma membrane. Implicated in breast carcinoma and prostate cancer. Biomarker of cervix uteri carcinoma in situ. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.306 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CADM1	NM_001301043.2	c.1112-3421A>G		intron_variant		ENST00000331581.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CADM1	ENST00000331581.11	c.1112-3421A>G		intron_variant		1	NM_001301043.2	P4

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29903 AN: 152072 Hom.: 3590 Cov.: 33

Gnomad AFR AF: 0.0682

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.197 AC: 29914 AN: 152190 Hom.: 3595 Cov.: 33 AF XY: 0.200 AC XY: 14847 AN XY: 74412

Gnomad4 AFR AF: 0.0681

Gnomad4 AMR AF: 0.283

Gnomad4 ASJ AF: 0.160

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.319

Gnomad4 FIN AF: 0.272

Gnomad4 NFE AF: 0.244

Gnomad4 OTH AF: 0.183

Alfa AF: 0.236 Hom.: 2094

Bravo AF: 0.189

Asia WGS AF: 0.219 AC: 760 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	3.4
Dann	Benign	0.30

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: rs11215406; hg19: chr11-115065082; COSMIC: COSV59003652; COSMIC: COSV59003652;