rs7177192
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_144508.5(KNL1):āc.128G>Cā(p.Arg43Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.805 in 1,539,926 control chromosomes in the GnomAD database, including 509,570 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 (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.128G>C | p.Arg43Thr | missense_variant | 4/26 | ENST00000399668.7 | |
KNL1 | NM_170589.5 | c.128G>C | p.Arg43Thr | missense_variant | 4/27 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KNL1 | ENST00000399668.7 | c.128G>C | p.Arg43Thr | missense_variant | 4/26 | 1 | NM_144508.5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.785 AC: 119256AN: 151964Hom.: 47776 Cov.: 32
GnomAD3 exomes AF: 0.737 AC: 183466AN: 248890Hom.: 71550 AF XY: 0.752 AC XY: 101611AN XY: 135054
GnomAD4 exome AF: 0.808 AC: 1120921AN: 1387844Hom.: 461756 Cov.: 22 AF XY: 0.809 AC XY: 561286AN XY: 693934
GnomAD4 genome ? AF: 0.785 AC: 119337AN: 152082Hom.: 47814 Cov.: 32 AF XY: 0.779 AC XY: 57943AN XY: 74336
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | May 23, 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 07, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at