chr11-115342006-C-T

Variant names:

• chr11-115342006-C-T
• rs7105871
• NM_001301043.2:c.125-101586G>A

Variant summary

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

The NM_001301043.2(CADM1):​c.125-101586G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.771 in 152,090 control chromosomes in the GnomAD database, including 45,407 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 0.77 (45407 hom., cov: 32)
• Consequence: CADM1 NM_001301043.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.457
• Publications: 4 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=-0.78).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CADM1	NM_001301043.2	c.125-101586G>A		intron_variant	Intron 1 of 11	ENST00000331581.11	NP_001287972.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CADM1	ENST00000331581.11	c.125-101586G>A		intron_variant	Intron 1 of 11	1	NM_001301043.2	ENSP00000329797.6

Frequencies

GnomAD3 genomes AF: 0.771 AC: 117137 AN: 151972 Hom.: 45346 Cov.: 32

Gnomad AFR AF: 0.799

Gnomad AMI AF: 0.712

Gnomad AMR AF: 0.810

Gnomad ASJ AF: 0.679

Gnomad EAS AF: 0.731

Gnomad SAS AF: 0.715

Gnomad FIN AF: 0.659

Gnomad MID AF: 0.742

Gnomad NFE AF: 0.774

Gnomad OTH AF: 0.781

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

GnomAD4 genome AF: 0.771 AC: 117260 AN: 152090 Hom.: 45407 Cov.: 32 AF XY: 0.766 AC XY: 56925 AN XY: 74326

African (AFR) AF: 0.800 AC: 33200 AN: 41518

American (AMR) AF: 0.810 AC: 12369 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.679 AC: 2353 AN: 3464

East Asian (EAS) AF: 0.732 AC: 3789 AN: 5176

South Asian (SAS) AF: 0.715 AC: 3440 AN: 4810

European-Finnish (FIN) AF: 0.659 AC: 6957 AN: 10554

Middle Eastern (MID) AF: 0.740 AC: 216 AN: 292

European-Non Finnish (NFE) AF: 0.774 AC: 52630 AN: 67984

Other (OTH) AF: 0.784 AC: 1657 AN: 2114

Alfa AF: 0.772 Hom.: 133890

Bravo AF: 0.786

Asia WGS AF: 0.732 AC: 2541 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	15
DANN	Benign	0.46
PhyloP100		0.46
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: rs7105871; hg19: chr11-115212725;