10-128102736-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002417.5(MKI67):c.9104C>T(p.Pro3035Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000031 in 1,614,036 control chromosomes in the GnomAD database, including 1 homozygotes. 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 (★).
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.9104C>T | p.Pro3035Leu | missense_variant | 13/15 | ENST00000368654.8 | NP_002408.3 | |
MKI67 | NM_001145966.2 | c.8024C>T | p.Pro2675Leu | missense_variant | 12/14 | NP_001139438.1 | ||
MKI67 | XM_011539818.3 | c.8072C>T | p.Pro2691Leu | missense_variant | 10/12 | XP_011538120.1 | ||
MKI67 | XM_006717864.4 | c.6782C>T | p.Pro2261Leu | missense_variant | 2/4 | XP_006717927.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MKI67 | ENST00000368654.8 | c.9104C>T | p.Pro3035Leu | missense_variant | 13/15 | 2 | NM_002417.5 | ENSP00000357643 | P2 | |
MKI67 | ENST00000368653.7 | c.8024C>T | p.Pro2675Leu | missense_variant | 12/14 | 2 | ENSP00000357642 | A2 | ||
MKI67 | ENST00000464771.1 | n.393C>T | non_coding_transcript_exon_variant | 1/2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152146Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251366Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135846
GnomAD4 exome AF: 0.0000322 AC: 47AN: 1461890Hom.: 1 Cov.: 36 AF XY: 0.0000344 AC XY: 25AN XY: 727244
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152146Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74318
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 16, 2021 | The c.9104C>T (p.P3035L) alteration is located in exon 13 (coding exon 12) of the MKI67 gene. This alteration results from a C to T substitution at nucleotide position 9104, causing the proline (P) at amino acid position 3035 to be replaced by a leucine (L). 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