rs201342316
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_198525.3(KIF7):c.3201G>T(p.Gln1067His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000754 in 1,459,514 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another nucleotide change resulting in same amino acid change has been previously reported as Uncertain significancein ClinVar. Synonymous variant affecting the same amino acid position (i.e. Q1067Q) has been classified as Likely benign.
Frequency
Consequence
NM_198525.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIF7 | NM_198525.3 | c.3201G>T | p.Gln1067His | missense_variant | 16/19 | ENST00000394412.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIF7 | ENST00000394412.8 | c.3201G>T | p.Gln1067His | missense_variant | 16/19 | 5 | NM_198525.3 | P2 | |
TICRR | ENST00000561095.1 | c.*1071C>A | 3_prime_UTR_variant, NMD_transcript_variant | 4/4 | 1 | ||||
KIF7 | ENST00000696512.1 | c.3324G>T | p.Gln1108His | missense_variant | 16/19 | A2 | |||
KIF7 | ENST00000677187.1 | n.875G>T | non_coding_transcript_exon_variant | 4/7 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000408 AC: 1AN: 245292Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 132686
GnomAD4 exome AF: 0.00000754 AC: 11AN: 1459514Hom.: 0 Cov.: 31 AF XY: 0.00000689 AC XY: 5AN XY: 725740
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Acrocallosal syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Feb 20, 2022 | 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 are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C15"). This variant has not been reported in the literature in individuals affected with KIF7-related conditions. This variant is present in population databases (rs201342316, gnomAD 0.0009%). This sequence change replaces glutamine, which is neutral and polar, with histidine, which is basic and polar, at codon 1067 of the KIF7 protein (p.Gln1067His). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at