chr10-128102724-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002417.5(MKI67):c.9116G>A(p.Gly3039Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000372 in 1,614,052 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 (★).
Frequency
Consequence
NM_002417.5 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MKI67 | NM_002417.5 | c.9116G>A | p.Gly3039Asp | missense_variant | Exon 13 of 15 | ENST00000368654.8 | NP_002408.3 | |
MKI67 | NM_001145966.2 | c.8036G>A | p.Gly2679Asp | missense_variant | Exon 12 of 14 | NP_001139438.1 | ||
MKI67 | XM_011539818.3 | c.8084G>A | p.Gly2695Asp | missense_variant | Exon 10 of 12 | XP_011538120.1 | ||
MKI67 | XM_006717864.4 | c.6794G>A | p.Gly2265Asp | missense_variant | Exon 2 of 4 | XP_006717927.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MKI67 | ENST00000368654.8 | c.9116G>A | p.Gly3039Asp | missense_variant | Exon 13 of 15 | 2 | NM_002417.5 | ENSP00000357643.3 | ||
MKI67 | ENST00000368653.7 | c.8036G>A | p.Gly2679Asp | missense_variant | Exon 12 of 14 | 2 | ENSP00000357642.3 | |||
MKI67 | ENST00000464771.1 | n.405G>A | non_coding_transcript_exon_variant | Exon 1 of 2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152164Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251422Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135870
GnomAD4 exome AF: 0.0000404 AC: 59AN: 1461888Hom.: 0 Cov.: 35 AF XY: 0.0000316 AC XY: 23AN XY: 727244
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152164Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74328
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.9116G>A (p.G3039D) alteration is located in exon 13 (coding exon 12) of the MKI67 gene. This alteration results from a G to A substitution at nucleotide position 9116, causing the glycine (G) at amino acid position 3039 to be replaced by an aspartic acid (D). 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