chr10-128102803-G-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_002417.5(MKI67):āc.9037C>Gā(p.Arg3013Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000591 in 152,190 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 (ā ).
Frequency
Consequence
NM_002417.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MKI67 | NM_002417.5 | c.9037C>G | p.Arg3013Gly | missense_variant | 13/15 | ENST00000368654.8 | |
MKI67 | NM_001145966.2 | c.7957C>G | p.Arg2653Gly | missense_variant | 12/14 | ||
MKI67 | XM_011539818.3 | c.8005C>G | p.Arg2669Gly | missense_variant | 10/12 | ||
MKI67 | XM_006717864.4 | c.6715C>G | p.Arg2239Gly | missense_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MKI67 | ENST00000368654.8 | c.9037C>G | p.Arg3013Gly | missense_variant | 13/15 | 2 | NM_002417.5 | P2 | |
MKI67 | ENST00000368653.7 | c.7957C>G | p.Arg2653Gly | missense_variant | 12/14 | 2 | A2 | ||
MKI67 | ENST00000464771.1 | n.326C>G | non_coding_transcript_exon_variant | 1/2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152190Hom.: 0 Cov.: 33
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000182 AC: 265AN: 1459612Hom.: 0 Cov.: 40 AF XY: 0.000172 AC XY: 125AN XY: 726092
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152190Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74338
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at