10-128099237-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_002417.5(MKI67):c.9724G>A(p.Val3242Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000149 in 1,613,092 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 Likely benign (★).
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MKI67 | NM_002417.5 | c.9724G>A | p.Val3242Ile | missense_variant | Exon 15 of 15 | ENST00000368654.8 | NP_002408.3 | |
MKI67 | NM_001145966.2 | c.8644G>A | p.Val2882Ile | missense_variant | Exon 14 of 14 | NP_001139438.1 | ||
MKI67 | XM_011539818.3 | c.8692G>A | p.Val2898Ile | missense_variant | Exon 12 of 12 | XP_011538120.1 | ||
MKI67 | XM_006717864.4 | c.7402G>A | p.Val2468Ile | missense_variant | Exon 4 of 4 | XP_006717927.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MKI67 | ENST00000368654.8 | c.9724G>A | p.Val3242Ile | missense_variant | Exon 15 of 15 | 2 | NM_002417.5 | ENSP00000357643.3 | ||
MKI67 | ENST00000368653.7 | c.8644G>A | p.Val2882Ile | missense_variant | Exon 14 of 14 | 2 | ENSP00000357642.3 |
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 15AN: 152130Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 248928Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 134790
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1460962Hom.: 0 Cov.: 29 AF XY: 0.00000826 AC XY: 6AN XY: 726790
GnomAD4 genome AF: 0.0000986 AC: 15AN: 152130Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 74310
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at