11-115209591-ATGGTGGTGGTGGTGGTGGTGG-ATGG
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP3BS2
The NM_001301043.2(CADM1):c.1043_1060delCCACCACCACCACCACCA(p.Thr348_Thr353del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.000014 in 785,844 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 0.0 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000014 ( 0 hom. )
Failed GnomAD Quality Control
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 GnomAdExome4 at 11 AD gene.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 139038Hom.: 0 Cov.: 32 FAILED QC
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GnomAD4 exome AF: 0.0000140 AC: 11AN: 785844Hom.: 0 AF XY: 0.00000977 AC XY: 4AN XY: 409312
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GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 139038Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 67276
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Data not reliable, filtered out with message: AC0
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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