rs138410949
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_198525.3(KIF7):c.2981A>G(p.Gln994Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00269 in 1,561,306 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q994H) 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 -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIF7 | NM_198525.3 | c.2981A>G | p.Gln994Arg | missense_variant | 15/19 | ENST00000394412.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIF7 | ENST00000394412.8 | c.2981A>G | p.Gln994Arg | missense_variant | 15/19 | 5 | NM_198525.3 | P2 | |
KIF7 | ENST00000696512.1 | c.3104A>G | p.Gln1035Arg | missense_variant | 15/19 | A2 | |||
KIF7 | ENST00000677187.1 | n.655A>G | non_coding_transcript_exon_variant | 3/7 |
Frequencies
GnomAD3 genomes ? AF: 0.00202 AC: 307AN: 152206Hom.: 1 Cov.: 34
GnomAD3 exomes AF: 0.00164 AC: 278AN: 169278Hom.: 1 AF XY: 0.00156 AC XY: 141AN XY: 90458
GnomAD4 exome AF: 0.00276 AC: 3894AN: 1408982Hom.: 8 Cov.: 39 AF XY: 0.00256 AC XY: 1780AN XY: 696186
GnomAD4 genome ? AF: 0.00202 AC: 307AN: 152324Hom.: 1 Cov.: 34 AF XY: 0.00196 AC XY: 146AN XY: 74494
ClinVar
Submissions by phenotype
not provided Uncertain:2Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 11, 2021 | In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 23891399, 26092869, 26648833, 21552264, 31322791) - |
Uncertain significance, flagged submission | clinical testing | Eurofins Ntd Llc (ga) | Nov 14, 2014 | - - |
Uncertain significance, flagged submission | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Mar 28, 2017 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | May 01, 2024 | KIF7: BP4, BS2 - |
Acrocallosal syndrome Pathogenic:1Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 26, 2024 | - - |
Pathogenic, flagged submission | research | UW Hindbrain Malformation Research Program, University of Washington | Feb 23, 2015 | - - |
Benign, 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. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign. - |
Intellectual disability Uncertain:1
Uncertain significance, flagged submission | clinical testing | Centre de Biologie Pathologie Génétique, Centre Hospitalier Universitaire de Lille | Jan 01, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at