chr5-132750975-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001039780.4(CCNI2):c.752C>T(p.Thr251Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000291 in 1,613,904 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. T251T) has been classified as Likely benign.
Frequency
Consequence
NM_001039780.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCNI2 | NM_001039780.4 | c.752C>T | p.Thr251Met | missense_variant | 4/6 | ENST00000378731.6 | |
SEPTIN8 | NM_001098811.2 | c.*1041G>A | 3_prime_UTR_variant | 10/10 | ENST00000378719.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCNI2 | ENST00000378731.6 | c.752C>T | p.Thr251Met | missense_variant | 4/6 | 1 | NM_001039780.4 | A2 | |
SEPTIN8 | ENST00000378719.7 | c.*1041G>A | 3_prime_UTR_variant | 10/10 | 1 | NM_001098811.2 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152246Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000717 AC: 18AN: 250948Hom.: 0 AF XY: 0.0000590 AC XY: 8AN XY: 135622
GnomAD4 exome AF: 0.0000274 AC: 40AN: 1461658Hom.: 0 Cov.: 30 AF XY: 0.0000289 AC XY: 21AN XY: 727120
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152246Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74386
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 27, 2024 | The c.752C>T (p.T251M) alteration is located in exon 4 (coding exon 4) of the CCNI2 gene. This alteration results from a C to T substitution at nucleotide position 752, causing the threonine (T) at amino acid position 251 to be replaced by a methionine (M). 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