11-115230847-C-T

Position:

• chr11-115230847-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.562+506G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.783 in 152,192 control chromosomes in the GnomAD database, including 47,343 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 0.78 (47343 hom., cov: 33)
• Consequence: CADM1 NM_001301043.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.24

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CADM1	NM_001301043.2	c.562+506G>A		intron_variant		ENST00000331581.11	NP_001287972.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CADM1	ENST00000331581.11	c.562+506G>A		intron_variant		1	NM_001301043.2	ENSP00000329797	P4

Frequencies

GnomAD3 genomes AF: 0.783 AC: 119071 AN: 152074 Hom.: 47290 Cov.: 33

Gnomad AFR AF: 0.789

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.827

Gnomad ASJ AF: 0.716

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.760

Gnomad FIN AF: 0.825

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.807

Gnomad OTH AF: 0.773

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

GnomAD4 genome AF: 0.783 AC: 119184 AN: 152192 Hom.: 47343 Cov.: 33 AF XY: 0.781 AC XY: 58142 AN XY: 74402

Gnomad4 AFR AF: 0.789

Gnomad4 AMR AF: 0.826

Gnomad4 ASJ AF: 0.716

Gnomad4 EAS AF: 0.317

Gnomad4 SAS AF: 0.762

Gnomad4 FIN AF: 0.825

Gnomad4 NFE AF: 0.807

Gnomad4 OTH AF: 0.773

Alfa AF: 0.777 Hom.: 4835

Bravo AF: 0.779

Asia WGS AF: 0.589 AC: 2048 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.036
DANN	Benign	0.66

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: rs10790068; hg19: chr11-115101567;