rs11215400

Variant names:

• chr11-115181915-A-C
• rs11215400
• NM_001301043.2:c.1166-3140T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 22 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 -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 rank	MANE	Protein	UniProt
CADM1	NM_001301043.2	c.1166-3140T>G		intron_variant	Intron 10 of 11	ENST00000331581.11	NP_001287972.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CADM1	ENST00000331581.11	c.1166-3140T>G		intron_variant	Intron 10 of 11	1	NM_001301043.2	ENSP00000329797.6

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

African (AFR) AF: 0.105 AC: 4359 AN: 41548

American (AMR) AF: 0.287 AC: 4385 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 591 AN: 3464

East Asian (EAS) AF: 0.142 AC: 735 AN: 5172

South Asian (SAS) AF: 0.323 AC: 1555 AN: 4820

European-Finnish (FIN) AF: 0.272 AC: 2880 AN: 10590

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.244 AC: 16596 AN: 67992

Other (OTH) AF: 0.193 AC: 409 AN: 2114

Alfa AF: 0.234 Hom.: 6739

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
PhyloP100		-1.3
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: rs11215400; hg19: chr11-115052635;