11-115209591-ATGGTGGTGGTGGTGGTGGTGG-ATGGTGGTGG
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP3BS2
The NM_001301043.2(CADM1):c.1049_1060delCCACCACCACCA(p.Thr350_Thr353del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.000105 in 924,880 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.00010 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00011 ( 0 hom. )
Consequence
CADM1
NM_001301043.2 disruptive_inframe_deletion
NM_001301043.2 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 6.96
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BP3
Nonframeshift variant in repetitive region in NM_001301043.2
BS2
High AC in GnomAd4 at 14 AD gene.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000101 AC: 14AN: 139038Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000146 AC: 31AN: 212678Hom.: 0 AF XY: 0.000121 AC XY: 14AN XY: 115448
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GnomAD4 exome AF: 0.000106 AC: 83AN: 785842Hom.: 0 AF XY: 0.0000928 AC XY: 38AN XY: 409310
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GnomAD4 genome AF: 0.000101 AC: 14AN: 139038Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 9AN XY: 67278
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ClinVar
Not reported inComputational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at