rs11858113
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_144508.5(KNL1):āc.1715T>Cā(p.Met572Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 1,613,456 control chromosomes in the GnomAD database, including 128,915 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_144508.5 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 |
---|---|---|---|---|---|---|---|
KNL1 | NM_144508.5 | c.1715T>C | p.Met572Thr | missense_variant | 10/26 | ENST00000399668.7 | |
KNL1 | NM_170589.5 | c.1793T>C | p.Met598Thr | missense_variant | 11/27 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KNL1 | ENST00000399668.7 | c.1715T>C | p.Met572Thr | missense_variant | 10/26 | 1 | NM_144508.5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.391 AC: 59385AN: 151990Hom.: 11787 Cov.: 32
GnomAD3 exomes AF: 0.386 AC: 96131AN: 248854Hom.: 19533 AF XY: 0.399 AC XY: 53865AN XY: 135030
GnomAD4 exome AF: 0.397 AC: 579650AN: 1461348Hom.: 117110 Cov.: 48 AF XY: 0.401 AC XY: 291601AN XY: 726978
GnomAD4 genome ? AF: 0.391 AC: 59439AN: 152108Hom.: 11805 Cov.: 32 AF XY: 0.393 AC XY: 29216AN XY: 74354
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Apr 25, 2013 | - - |
Primary Microcephaly, Recessive Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Microcephaly 4, primary, autosomal recessive Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 14, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 20, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at