chr3-85883320-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001256502.2(CADM2):c.-84C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000682 in 1,613,434 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001256502.2 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CADM2 | ENST00000383699.8 | c.268C>T | p.Arg90Cys | missense_variant | Exon 4 of 10 | 1 | NM_001167675.2 | ENSP00000373200.3 | ||
CADM2 | ENST00000405615.2 | c.247C>T | p.Arg83Cys | missense_variant | Exon 3 of 10 | 1 | ENSP00000384193.2 | |||
CADM2 | ENST00000407528.6 | c.241C>T | p.Arg81Cys | missense_variant | Exon 3 of 10 | 1 | ENSP00000384575.2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152060Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 250796Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135546
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461256Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 726902
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152178Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74390
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.247C>T (p.R83C) alteration is located in exon 3 (coding exon 3) of the CADM2 gene. This alteration results from a C to T substitution at nucleotide position 247, causing the arginine (R) at amino acid position 83 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at