rs147191956
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2
The NM_198525.3(KIF7):c.3202C>T(p.Arg1068Trp) variant causes a missense change. The variant allele was found at a frequency of 0.000317 in 1,611,870 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1068Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_198525.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIF7 | NM_198525.3 | c.3202C>T | p.Arg1068Trp | missense_variant | 16/19 | ENST00000394412.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIF7 | ENST00000394412.8 | c.3202C>T | p.Arg1068Trp | missense_variant | 16/19 | 5 | NM_198525.3 | P2 | |
TICRR | ENST00000561095.1 | c.*1070G>A | 3_prime_UTR_variant, NMD_transcript_variant | 4/4 | 1 | ||||
KIF7 | ENST00000696512.1 | c.3325C>T | p.Arg1109Trp | missense_variant | 16/19 | A2 | |||
KIF7 | ENST00000677187.1 | n.876C>T | non_coding_transcript_exon_variant | 4/7 |
Frequencies
GnomAD3 genomes ? AF: 0.000282 AC: 43AN: 152234Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000420 AC: 103AN: 245332Hom.: 1 AF XY: 0.000452 AC XY: 60AN XY: 132712
GnomAD4 exome AF: 0.000321 AC: 468AN: 1459518Hom.: 5 Cov.: 31 AF XY: 0.000358 AC XY: 260AN XY: 725714
GnomAD4 genome ? AF: 0.000282 AC: 43AN: 152352Hom.: 0 Cov.: 33 AF XY: 0.000322 AC XY: 24AN XY: 74510
ClinVar
Submissions by phenotype
Acrocallosal syndrome Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 19, 2023 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Jan 23, 2020 | Identified as a single heterozygous variant in an individual with Bardet-Biedl syndrome who also harbored two frameshift variants in the BBS9 gene (Putoux et al., 2011); Identified in an individual with a favorable disease course as part of a study evaluating genetic variants in individuals with favorable or poor disease course after sepsis (Taudien et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 21552264, 27639823) - |
KIF7-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 23, 2020 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at