chr11-115173356-G-A

Position:

• chr11-115173356-G-A

Variant summary

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

The ENST00000331581.11(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 ENST00000331581.11 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.918

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=-0.84).
• 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/exons	MANE	Protein	UniProt
CADM1	NM_001301043.2	c.*3118C>T		3_prime_UTR_variant	12/12	ENST00000331581.11	NP_001287972.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CADM1	ENST00000331581.11	c.*3118C>T		3_prime_UTR_variant	12/12	1	NM_001301043.2	ENSP00000329797	P4

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

Gnomad4 AFR exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.700

Gnomad4 NFE exome AF: 0.652

Gnomad4 OTH exome AF: 0.250

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

Gnomad4 AFR AF: 0.266

Gnomad4 AMR AF: 0.395

Gnomad4 ASJ AF: 0.488

Gnomad4 EAS AF: 0.198

Gnomad4 SAS AF: 0.407

Gnomad4 FIN AF: 0.499

Gnomad4 NFE AF: 0.531

Gnomad4 OTH AF: 0.438

Alfa AF: 0.484 Hom.: 5585

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

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: rs11215397; hg19: chr11-115044076;