3-108554433-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020890.3(CIP2A):āc.2267A>Gā(p.Asn756Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000212 in 1,416,918 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 (ā ).
Frequency
Consequence
NM_020890.3 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 |
---|---|---|---|---|---|---|---|
CIP2A | NM_020890.3 | c.2267A>G | p.Asn756Ser | missense_variant | 18/21 | ENST00000295746.13 | |
CIP2A | XM_006713716.4 | c.2264A>G | p.Asn755Ser | missense_variant | 18/21 | ||
CIP2A | XM_011513057.3 | c.1325A>G | p.Asn442Ser | missense_variant | 11/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CIP2A | ENST00000295746.13 | c.2267A>G | p.Asn756Ser | missense_variant | 18/21 | 1 | NM_020890.3 | P1 | |
CIP2A | ENST00000491772.5 | c.1790A>G | p.Asn597Ser | missense_variant | 18/21 | 1 | |||
CIP2A | ENST00000481530.5 | c.*1837A>G | 3_prime_UTR_variant, NMD_transcript_variant | 18/21 | 1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.00000432 AC: 1AN: 231730Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 124532
GnomAD4 exome AF: 0.00000212 AC: 3AN: 1416918Hom.: 0 Cov.: 24 AF XY: 0.00000283 AC XY: 2AN XY: 705794
GnomAD4 genome Cov.: 31
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at