15-89645125-G-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6BP7
The NM_198525.3(KIF7):c.2079C>A(p.Val693=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000766 in 1,605,120 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. V693V) has been classified as Likely benign.
Frequency
Consequence
NM_198525.3 synonymous
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 |
---|---|---|---|---|---|---|---|
KIF7 | NM_198525.3 | c.2079C>A | p.Val693= | synonymous_variant | 10/19 | ENST00000394412.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIF7 | ENST00000394412.8 | c.2079C>A | p.Val693= | synonymous_variant | 10/19 | 5 | NM_198525.3 | P2 | |
KIF7 | ENST00000696512.1 | c.2202C>A | p.Val734= | synonymous_variant | 10/19 | A2 |
Frequencies
GnomAD3 genomes AF: 0.000282 AC: 43AN: 152230Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000904 AC: 22AN: 243332Hom.: 0 AF XY: 0.0000755 AC XY: 10AN XY: 132522
GnomAD4 exome AF: 0.0000558 AC: 81AN: 1452772Hom.: 1 Cov.: 32 AF XY: 0.0000512 AC XY: 37AN XY: 723174
GnomAD4 genome AF: 0.000276 AC: 42AN: 152348Hom.: 0 Cov.: 32 AF XY: 0.000255 AC XY: 19AN XY: 74498
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Jul 12, 2023 | In silico analysis supports that this variant does not alter splicing; Has not been previously published as pathogenic or benign to our knowledge - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Acrocallosal syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 14, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at