11-115209591-ATGGTGGTGGTGGTGGTGGTGG-ATGGTGGTGGTGGTGG
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP3BS2
The NM_001301043.2(CADM1):c.1055_1060delCCACCA(p.Thr352_Thr353del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.0000541 in 924,238 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 0.000036 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000057 ( 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: 5.44
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 5 AD gene.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000360 AC: 5AN: 139038Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.0000573 AC: 45AN: 785076Hom.: 0 AF XY: 0.0000538 AC XY: 22AN XY: 408986
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GnomAD4 genome AF: 0.0000359 AC: 5AN: 139162Hom.: 0 Cov.: 32 AF XY: 0.0000445 AC XY: 3AN XY: 67384
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ClinVar
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at