rs116942055
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_004523.4(KIF11):c.2153A>T(p.His718Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000824 in 1,599,684 control chromosomes in the GnomAD database, including 27 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. H718H) has been classified as Likely benign.
Frequency
Consequence
NM_004523.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIF11 | NM_004523.4 | c.2153A>T | p.His718Leu | missense_variant | 16/22 | ENST00000260731.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIF11 | ENST00000260731.5 | c.2153A>T | p.His718Leu | missense_variant | 16/22 | 1 | NM_004523.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00123 AC: 187AN: 152224Hom.: 5 Cov.: 33
GnomAD3 exomes AF: 0.00254 AC: 598AN: 235036Hom.: 10 AF XY: 0.00241 AC XY: 306AN XY: 127114
GnomAD4 exome AF: 0.000781 AC: 1130AN: 1447340Hom.: 22 Cov.: 32 AF XY: 0.000750 AC XY: 540AN XY: 719646
GnomAD4 genome ? AF: 0.00123 AC: 188AN: 152344Hom.: 5 Cov.: 33 AF XY: 0.00134 AC XY: 100AN XY: 74498
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 15, 2020 | - - |
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2022 | KIF11: PS2:Supporting, BP4, BS1, BS2 - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Microcephaly with or without chorioretinopathy, lymphedema, or intellectual disability Benign:2
Benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Aug 16, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | Oct 12, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at