5-132747626-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001039780.4(CCNI2):c.131G>A(p.Gly44Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000018 in 1,501,924 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001039780.4 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCNI2 | NM_001039780.4 | c.131G>A | p.Gly44Glu | missense_variant | 1/6 | ENST00000378731.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCNI2 | ENST00000378731.6 | c.131G>A | p.Gly44Glu | missense_variant | 1/6 | 1 | NM_001039780.4 | A2 | |
CCNI2 | ENST00000614847.1 | c.131G>A | p.Gly44Glu | missense_variant | 1/6 | 1 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000854 AC: 13AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000103 AC: 1AN: 97296Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 54728
GnomAD4 exome AF: 0.0000104 AC: 14AN: 1349740Hom.: 0 Cov.: 31 AF XY: 0.00000901 AC XY: 6AN XY: 665566
GnomAD4 genome ? AF: 0.0000854 AC: 13AN: 152184Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74358
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 06, 2023 | The c.131G>A (p.G44E) alteration is located in exon 1 (coding exon 1) of the CCNI2 gene. This alteration results from a G to A substitution at nucleotide position 131, causing the glycine (G) at amino acid position 44 to be replaced by a glutamic acid (E). 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