chr5-132750891-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001039780.4(CCNI2):c.668A>G(p.Tyr223Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000104 in 1,614,160 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 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.668A>G | p.Tyr223Cys | missense_variant | 4/6 | ENST00000378731.6 | |
SEPTIN8 | NM_001098811.2 | c.*1125T>C | 3_prime_UTR_variant | 10/10 | ENST00000378719.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCNI2 | ENST00000378731.6 | c.668A>G | p.Tyr223Cys | missense_variant | 4/6 | 1 | NM_001039780.4 | A2 | |
SEPTIN8 | ENST00000378719.7 | c.*1125T>C | 3_prime_UTR_variant | 10/10 | 1 | NM_001098811.2 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000854 AC: 13AN: 152280Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000756 AC: 19AN: 251462Hom.: 0 AF XY: 0.0000957 AC XY: 13AN XY: 135906
GnomAD4 exome AF: 0.000106 AC: 155AN: 1461880Hom.: 2 Cov.: 30 AF XY: 0.000121 AC XY: 88AN XY: 727244
GnomAD4 genome ? AF: 0.0000854 AC: 13AN: 152280Hom.: 0 Cov.: 33 AF XY: 0.0000806 AC XY: 6AN XY: 74400
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 16, 2021 | The c.668A>G (p.Y223C) alteration is located in exon 4 (coding exon 4) of the CCNI2 gene. This alteration results from a A to G substitution at nucleotide position 668, causing the tyrosine (Y) at amino acid position 223 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