10-128101541-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.9422G>A(p.Arg3141Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000198 in 1,614,100 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MKI67 | NM_002417.5 | c.9422G>A | p.Arg3141Gln | missense_variant | 14/15 | ENST00000368654.8 | NP_002408.3 | |
MKI67 | NM_001145966.2 | c.8342G>A | p.Arg2781Gln | missense_variant | 13/14 | NP_001139438.1 | ||
MKI67 | XM_011539818.3 | c.8390G>A | p.Arg2797Gln | missense_variant | 11/12 | XP_011538120.1 | ||
MKI67 | XM_006717864.4 | c.7100G>A | p.Arg2367Gln | missense_variant | 3/4 | XP_006717927.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MKI67 | ENST00000368654.8 | c.9422G>A | p.Arg3141Gln | missense_variant | 14/15 | 2 | NM_002417.5 | ENSP00000357643.3 | ||
MKI67 | ENST00000368653.7 | c.8342G>A | p.Arg2781Gln | missense_variant | 13/14 | 2 | ENSP00000357642.3 | |||
MKI67 | ENST00000464771.1 | n.635G>A | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152210Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251386Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135868
GnomAD4 exome AF: 0.0000171 AC: 25AN: 1461890Hom.: 0 Cov.: 34 AF XY: 0.0000124 AC XY: 9AN XY: 727248
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152210Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74358
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 14, 2024 | The c.9422G>A (p.R3141Q) alteration is located in exon 14 (coding exon 13) of the MKI67 gene. This alteration results from a G to A substitution at nucleotide position 9422, causing the arginine (R) at amino acid position 3141 to be replaced by a glutamine (Q). 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