rs7105871

chr11-115342006-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.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

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=-0.78).
• 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/exons	MANE	UniProt
CADM1	NM_001301043.2	c.125-101586G>A		intron_variant		ENST00000331581.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CADM1	ENST00000331581.11	c.125-101586G>A		intron_variant		1	NM_001301043.2	P4

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

Gnomad4 AFR AF: 0.800

Gnomad4 AMR AF: 0.810

Gnomad4 ASJ AF: 0.679

Gnomad4 EAS AF: 0.732

Gnomad4 SAS AF: 0.715

Gnomad4 FIN AF: 0.659

Gnomad4 NFE AF: 0.774

Gnomad4 OTH AF: 0.784

Alfa AF: 0.767 Hom.: 84893

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

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: rs7105871; hg19: chr11-115212725;