10-128102750-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002417.5(MKI67):āc.9090G>Cā(p.Lys3030Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,614,248 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_002417.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MKI67 | NM_002417.5 | c.9090G>C | p.Lys3030Asn | missense_variant | 13/15 | ENST00000368654.8 | NP_002408.3 | |
MKI67 | NM_001145966.2 | c.8010G>C | p.Lys2670Asn | missense_variant | 12/14 | NP_001139438.1 | ||
MKI67 | XM_011539818.3 | c.8058G>C | p.Lys2686Asn | missense_variant | 10/12 | XP_011538120.1 | ||
MKI67 | XM_006717864.4 | c.6768G>C | p.Lys2256Asn | missense_variant | 2/4 | XP_006717927.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MKI67 | ENST00000368654.8 | c.9090G>C | p.Lys3030Asn | missense_variant | 13/15 | 2 | NM_002417.5 | ENSP00000357643 | P2 | |
MKI67 | ENST00000368653.7 | c.8010G>C | p.Lys2670Asn | missense_variant | 12/14 | 2 | ENSP00000357642 | A2 | ||
MKI67 | ENST00000464771.1 | n.379G>C | non_coding_transcript_exon_variant | 1/2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152236Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251378Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135848
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461894Hom.: 0 Cov.: 36 AF XY: 0.00 AC XY: 0AN XY: 727248
GnomAD4 genome AF: 0.00000656 AC: 1AN: 152354Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74502
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 20, 2024 | The c.9090G>C (p.K3030N) alteration is located in exon 13 (coding exon 12) of the MKI67 gene. This alteration results from a G to C substitution at nucleotide position 9090, causing the lysine (K) at amino acid position 3030 to be replaced by an asparagine (N). 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