rs144726295
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_144508.5(KNL1):āc.1129A>Gā(p.Ile377Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000525 in 1,612,178 control chromosomes in the GnomAD database, including 2 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 Likely 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KNL1 | NM_144508.5 | c.1129A>G | p.Ile377Val | missense_variant | 10/26 | ENST00000399668.7 | NP_653091.3 | |
KNL1 | NM_170589.5 | c.1207A>G | p.Ile403Val | missense_variant | 11/27 | NP_733468.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KNL1 | ENST00000399668.7 | c.1129A>G | p.Ile377Val | missense_variant | 10/26 | 1 | NM_144508.5 | ENSP00000382576.3 |
Frequencies
GnomAD3 genomes AF: 0.00294 AC: 448AN: 152230Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000718 AC: 177AN: 246676Hom.: 0 AF XY: 0.000492 AC XY: 66AN XY: 134140
GnomAD4 exome AF: 0.000273 AC: 398AN: 1459830Hom.: 2 Cov.: 33 AF XY: 0.000244 AC XY: 177AN XY: 726092
GnomAD4 genome AF: 0.00294 AC: 448AN: 152348Hom.: 0 Cov.: 32 AF XY: 0.00298 AC XY: 222AN XY: 74508
ClinVar
Submissions by phenotype
not specified Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | May 24, 2017 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | May 23, 2017 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 31, 2019 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | May 01, 2023 | KNL1: BP4, BS1 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at