rs11215400

chr11-115181915-A-C

Variant summary

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

The NM_001301043.2(CADM1):c.1166-3140T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 152,188 control chromosomes in the GnomAD database, including 3,789 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 0.21 (3789 hom., cov: 32)
• Consequence: CADM1 NM_001301043.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33

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 = 0.309 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CADM1	NM_001301043.2	c.1166-3140T>G		intron_variant		ENST00000331581.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CADM1	ENST00000331581.11	c.1166-3140T>G		intron_variant		1	NM_001301043.2	P4

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31631 AN: 152070 Hom.: 3784 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.0714

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.208 AC: 31642 AN: 152188 Hom.: 3789 Cov.: 32 AF XY: 0.211 AC XY: 15681 AN XY: 74410

Gnomad4 AFR AF: 0.105

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.171

Gnomad4 EAS AF: 0.142

Gnomad4 SAS AF: 0.323

Gnomad4 FIN AF: 0.272

Gnomad4 NFE AF: 0.244

Gnomad4 OTH AF: 0.193

Alfa AF: 0.212 Hom.: 439

Bravo AF: 0.202

Asia WGS AF: 0.230 AC: 798 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	0.13
Dann	Benign	0.44

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: rs11215400; hg19: chr11-115052635;