rs11215397

Variant names:

• chr11-115173356-G-A
• rs11215397
• NM_001301043.2:c.*3118C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001301043.2(CADM1):​c.*3118C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 152,158 control chromosomes in the GnomAD database, including 15,012 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 0.43 (14986 hom., cov: 33)
  • Exomes 𝑓: 0.60 (26 hom.)
• Consequence: CADM1 NM_001301043.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.918
• Publications: 5 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.527 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CADM1	NM_001301043.2	c.*3118C>T		3_prime_UTR_variant	Exon 12 of 12	ENST00000331581.11	NP_001287972.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CADM1	ENST00000331581.11	c.*3118C>T		3_prime_UTR_variant	Exon 12 of 12	1	NM_001301043.2	ENSP00000329797.6

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64628 AN: 151922 Hom.: 14984 Cov.: 33

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.499

Gnomad MID AF: 0.379

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.442

GnomAD4 exome AF: 0.602 AC: 71 AN: 118 Hom.: 26 Cov.: 0 AF XY: 0.625 AC XY: 60 AN XY: 96

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 4

South Asian (SAS) AF: 1.00 AC: 2 AN: 2

European-Finnish (FIN) AF: 0.700 AC: 7 AN: 10

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.652 AC: 60 AN: 92

Other (OTH) AF: 0.250 AC: 2 AN: 8

GnomAD4 genome AF: 0.425 AC: 64638 AN: 152040 Hom.: 14986 Cov.: 33 AF XY: 0.424 AC XY: 31484 AN XY: 74316

African (AFR) AF: 0.266 AC: 11045 AN: 41500

American (AMR) AF: 0.395 AC: 6037 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.488 AC: 1691 AN: 3468

East Asian (EAS) AF: 0.198 AC: 1020 AN: 5152

South Asian (SAS) AF: 0.407 AC: 1958 AN: 4816

European-Finnish (FIN) AF: 0.499 AC: 5282 AN: 10588

Middle Eastern (MID) AF: 0.384 AC: 112 AN: 292

European-Non Finnish (NFE) AF: 0.531 AC: 36086 AN: 67932

Other (OTH) AF: 0.438 AC: 922 AN: 2106

Alfa AF: 0.481 Hom.: 6922

Bravo AF: 0.410

Asia WGS AF: 0.274 AC: 955 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.2
DANN	Benign	0.88
PhyloP100		0.92
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: rs11215397; hg19: chr11-115044076;