10-128101371-T-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002417.5(MKI67):c.9592A>T(p.Met3198Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,614,086 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M3198K) has been classified 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MKI67 | NM_002417.5 | c.9592A>T | p.Met3198Leu | missense_variant | 14/15 | ENST00000368654.8 | |
MKI67 | NM_001145966.2 | c.8512A>T | p.Met2838Leu | missense_variant | 13/14 | ||
MKI67 | XM_011539818.3 | c.8560A>T | p.Met2854Leu | missense_variant | 11/12 | ||
MKI67 | XM_006717864.4 | c.7270A>T | p.Met2424Leu | missense_variant | 3/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MKI67 | ENST00000368654.8 | c.9592A>T | p.Met3198Leu | missense_variant | 14/15 | 2 | NM_002417.5 | P2 | |
MKI67 | ENST00000368653.7 | c.8512A>T | p.Met2838Leu | missense_variant | 13/14 | 2 | A2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152238Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251432Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135882
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461848Hom.: 0 Cov.: 62 AF XY: 0.00 AC XY: 0AN XY: 727226
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152238Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74368
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at