4-17814897-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_022346.5(NCAPG):c.589C>T(p.Arg197Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000149 in 1,613,942 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R197Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_022346.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NCAPG | NM_022346.5 | c.589C>T | p.Arg197Trp | missense_variant | 4/21 | ENST00000251496.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NCAPG | ENST00000251496.7 | c.589C>T | p.Arg197Trp | missense_variant | 4/21 | 1 | NM_022346.5 | P1 | |
NCAPG | ENST00000514176.5 | c.589C>T | p.Arg197Trp | missense_variant, NMD_transcript_variant | 4/20 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152110Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251390Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135884
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461832Hom.: 0 Cov.: 31 AF XY: 0.0000151 AC XY: 11AN XY: 727216
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152110Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74292
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 27, 2022 | The c.589C>T (p.R197W) alteration is located in exon 4 (coding exon 4) of the NCAPG gene. This alteration results from a C to T substitution at nucleotide position 589, causing the arginine (R) at amino acid position 197 to be replaced by a tryptophan (W). 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