chr3-12807362-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001162499.2(CAND2):c.269C>T(p.Thr90Ile) variant causes a missense change. The variant allele was found at a frequency of 0.000416 in 1,551,748 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001162499.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CAND2 | NM_001162499.2 | c.269C>T | p.Thr90Ile | missense_variant | Exon 3 of 15 | ENST00000456430.6 | NP_001155971.1 | |
CAND2 | XM_011533504.3 | c.197C>T | p.Thr66Ile | missense_variant | Exon 3 of 15 | XP_011531806.1 | ||
CAND2 | XM_011533503.3 | c.269C>T | p.Thr90Ile | missense_variant | Exon 3 of 14 | XP_011531805.1 | ||
CAND2 | NM_012298.3 | c.213-2697C>T | intron_variant | Intron 2 of 12 | NP_036430.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000407 AC: 62AN: 152204Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000536 AC: 84AN: 156690Hom.: 0 AF XY: 0.000494 AC XY: 41AN XY: 82990
GnomAD4 exome AF: 0.000417 AC: 584AN: 1399426Hom.: 0 Cov.: 34 AF XY: 0.000406 AC XY: 280AN XY: 690216
GnomAD4 genome AF: 0.000407 AC: 62AN: 152322Hom.: 0 Cov.: 33 AF XY: 0.000483 AC XY: 36AN XY: 74488
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.269C>T (p.T90I) alteration is located in exon 3 (coding exon 3) of the CAND2 gene. This alteration results from a C to T substitution at nucleotide position 269, causing the threonine (T) at amino acid position 90 to be replaced by an isoleucine (I). 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