4-17818048-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_022346.5(NCAPG):c.1078A>G(p.Ile360Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000205 in 1,613,218 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/23 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_022346.5 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 |
---|---|---|---|---|---|---|---|
NCAPG | NM_022346.5 | c.1078A>G | p.Ile360Val | missense_variant | 7/21 | ENST00000251496.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NCAPG | ENST00000251496.7 | c.1078A>G | p.Ile360Val | missense_variant | 7/21 | 1 | NM_022346.5 | P1 | |
NCAPG | ENST00000514176.5 | c.*294A>G | 3_prime_UTR_variant, NMD_transcript_variant | 6/20 | 1 | ||||
NCAPG | ENST00000509719.1 | n.332A>G | non_coding_transcript_exon_variant | 2/3 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152118Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000798 AC: 20AN: 250530Hom.: 0 AF XY: 0.0000591 AC XY: 8AN XY: 135456
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1461100Hom.: 0 Cov.: 31 AF XY: 0.0000165 AC XY: 12AN XY: 726838
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152118Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74292
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 24, 2022 | The c.1078A>G (p.I360V) alteration is located in exon 7 (coding exon 7) of the NCAPG gene. This alteration results from a A to G substitution at nucleotide position 1078, causing the isoleucine (I) at amino acid position 360 to be replaced by a valine (V). 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