rs3802858

Positions:

• chr11-115207772-T-C
• chr11-115207772-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001301043.2(CADM1):​c.1078+1802A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 151,996 control chromosomes in the GnomAD database, including 12,717 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 0.41 (12717 hom., cov: 32)
• Consequence: CADM1 NM_001301043.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CADM1	NM_001301043.2	c.1078+1802A>G		intron_variant		ENST00000331581.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CADM1	ENST00000331581.11	c.1078+1802A>G		intron_variant		1	NM_001301043.2	P4

Frequencies

GnomAD3 genomes AF: 0.406 AC: 61637 AN: 151876 Hom.: 12709 Cov.: 32

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.406 AC: 61668 AN: 151996 Hom.: 12717 Cov.: 32 AF XY: 0.406 AC XY: 30196 AN XY: 74312

Gnomad4 AFR AF: 0.344

Gnomad4 AMR AF: 0.447

Gnomad4 ASJ AF: 0.397

Gnomad4 EAS AF: 0.438

Gnomad4 SAS AF: 0.442

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.423

Gnomad4 OTH AF: 0.402

Alfa AF: 0.403 Hom.: 1506

Bravo AF: 0.405

Asia WGS AF: 0.435 AC: 1513 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.096
DANN	Benign	0.60

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: rs3802858; hg19: chr11-115078492;