rs10891802

chr11-115173168-C-Achr11-115173168-C-Gchr11-115173168-C-T

Variant summary

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

The NM_001301043.2(CADM1):c.*3306G>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 0.442 in 151,878 control chromosomes in the GnomAD database, including 16,007 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 0.44 (15996 hom., cov: 31)
  • Exomes 𝑓: 0.51 (11 hom.)
• Consequence: CADM1 NM_001301043.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.809

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.524 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CADM1	NM_001301043.2	c.*3306G>T		3_prime_UTR_variant	12/12	ENST00000331581.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CADM1	ENST00000331581.11	c.*3306G>T		3_prime_UTR_variant	12/12	1	NM_001301043.2	P4

Frequencies

GnomAD3 genomes AF: 0.442 AC: 67021 AN: 151684 Hom.: 15998 Cov.: 31

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.531

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.462

GnomAD4 exome AF: 0.513 AC: 40 AN: 78 Hom.: 11 Cov.: 0 AF XY: 0.516 AC XY: 33 AN XY: 64

Gnomad4 AFR exome AF: 0.500

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.250

Gnomad4 EAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.667

Gnomad4 NFE exome AF: 0.565

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.442 AC: 67031 AN: 151800 Hom.: 15996 Cov.: 31 AF XY: 0.445 AC XY: 33002 AN XY: 74174

Gnomad4 AFR AF: 0.266

Gnomad4 AMR AF: 0.406

Gnomad4 ASJ AF: 0.506

Gnomad4 EAS AF: 0.488

Gnomad4 SAS AF: 0.514

Gnomad4 FIN AF: 0.531

Gnomad4 NFE AF: 0.528

Gnomad4 OTH AF: 0.458

Alfa AF: 0.505 Hom.: 28966

Bravo AF: 0.424

Asia WGS AF: 0.445 AC: 1546 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	6.8
Dann	Benign	0.66

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs10891802; hg19: chr11-115043888;