rs11215416

Variant names:

• chr11-115206607-A-G
• rs11215416
• NM_001301043.2:c.1078+2967T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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]

CADM1 Gene-Disease associations (from GenCC):

• autism spectrum disorder

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CADM1	NM_001301043.2	c.1078+2967T>C		intron_variant	Intron 8 of 11	ENST00000331581.11	NP_001287972.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CADM1	ENST00000331581.11	c.1078+2967T>C		intron_variant	Intron 8 of 11	1	NM_001301043.2	ENSP00000329797.6

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

African (AFR) AF: 0.0682 AC: 2831 AN: 41520

American (AMR) AF: 0.281 AC: 4293 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 553 AN: 3466

East Asian (EAS) AF: 0.143 AC: 736 AN: 5158

South Asian (SAS) AF: 0.315 AC: 1516 AN: 4806

European-Finnish (FIN) AF: 0.272 AC: 2870 AN: 10562

Middle Eastern (MID) AF: 0.216 AC: 63 AN: 292

European-Non Finnish (NFE) AF: 0.244 AC: 16566 AN: 67960

Other (OTH) AF: 0.184 AC: 388 AN: 2108

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
PhyloP100		0.18
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: rs11215416; hg19: chr11-115077327;