rs220842

chr11-115411454-A-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001301043.2(CADM1):c.124+92817T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.967 in 152,248 control chromosomes in the GnomAD database, including 71,483 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 0.97 (71483 hom., cov: 31)
• Consequence: CADM1 NM_001301043.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.391

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.988 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CADM1	NM_001301043.2	c.124+92817T>A		intron_variant		ENST00000331581.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CADM1	ENST00000331581.11	c.124+92817T>A		intron_variant		1	NM_001301043.2	P4

Frequencies

GnomAD3 genomes AF: 0.967 AC: 147139 AN: 152130 Hom.: 71421 Cov.: 31

Gnomad AFR AF: 0.996

Gnomad AMI AF: 0.985

Gnomad AMR AF: 0.959

Gnomad ASJ AF: 0.967

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.920

Gnomad FIN AF: 0.849

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.989

Gnomad OTH AF: 0.980

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

GnomAD4 genome AF: 0.967 AC: 147261 AN: 152248 Hom.: 71483 Cov.: 31 AF XY: 0.958 AC XY: 71304 AN XY: 74412

Gnomad4 AFR AF: 0.996

Gnomad4 AMR AF: 0.959

Gnomad4 ASJ AF: 0.967

Gnomad4 EAS AF: 0.746

Gnomad4 SAS AF: 0.921

Gnomad4 FIN AF: 0.849

Gnomad4 NFE AF: 0.989

Gnomad4 OTH AF: 0.979

Alfa AF: 0.981 Hom.: 9099

Bravo AF: 0.977

Asia WGS AF: 0.848 AC: 2946 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
Cadd	Benign	16
Dann	Benign	0.76

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: rs220842; hg19: chr11-115282172;