rs11215416

Positions:

• chr11-115206607-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001301043.2(CADM1):​c.1078+2967T>C 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 152,044 control chromosomes in the GnomAD database, including 3,564 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 (3564 hom., cov: 31)
• Consequence: CADM1 NM_001301043.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CADM1	NM_001301043.2	c.1078+2967T>C		intron_variant		ENST00000331581.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CADM1	ENST00000331581.11	c.1078+2967T>C		intron_variant		1	NM_001301043.2	P4

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29872 AN: 151926 Hom.: 3559 Cov.: 31

Gnomad AFR AF: 0.0683

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.197 AC: 29882 AN: 152044 Hom.: 3564 Cov.: 31 AF XY: 0.200 AC XY: 14823 AN XY: 74300

Gnomad4 AFR AF: 0.0682

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.160

Gnomad4 EAS AF: 0.143

Gnomad4 SAS AF: 0.315

Gnomad4 FIN AF: 0.272

Gnomad4 NFE AF: 0.244

Gnomad4 OTH AF: 0.184

Alfa AF: 0.212 Hom.: 754

Bravo AF: 0.189

Asia WGS AF: 0.222 AC: 773 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	14
DANN	Benign	0.70

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: rs11215416; hg19: chr11-115077327;