chr15-89629411-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_198525.3(KIF7):āc.3481G>Cā(p.Glu1161Gln) variant causes a missense change. The variant allele was found at a frequency of 0.00000275 in 1,453,636 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E1161K) has been classified as Uncertain significance.
Frequency
Consequence
NM_198525.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIF7 | NM_198525.3 | c.3481G>C | p.Glu1161Gln | missense_variant | 17/19 | ENST00000394412.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIF7 | ENST00000394412.8 | c.3481G>C | p.Glu1161Gln | missense_variant | 17/19 | 5 | NM_198525.3 | P2 | |
TICRR | ENST00000561095.1 | c.*97-19C>G | intron_variant, NMD_transcript_variant | 1 | |||||
KIF7 | ENST00000696512.1 | c.3604G>C | p.Glu1202Gln | missense_variant | 17/19 | A2 | |||
KIF7 | ENST00000677187.1 | n.1155G>C | non_coding_transcript_exon_variant | 5/7 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000275 AC: 4AN: 1453636Hom.: 0 Cov.: 37 AF XY: 0.00000138 AC XY: 1AN XY: 723482
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Acrocallosal syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Dec 22, 2020 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant has not been reported in the literature in individuals with KIF7-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces glutamic acid with glutamine at codon 1161 of the KIF7 protein (p.Glu1161Gln). The glutamic acid residue is highly conserved and there is a small physicochemical difference between glutamic acid and glutamine. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at