rs142957638
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_StrongBP6BS1
The NM_206937.2(LIG4):c.686A>G(p.His229Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000313 in 1,613,382 control chromosomes in the GnomAD database, including 1 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 Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. H229H) has been classified as Likely benign.
Frequency
Consequence
NM_206937.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LIG4 | NM_206937.2 | c.686A>G | p.His229Arg | missense_variant | 3/3 | ENST00000442234.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LIG4 | ENST00000442234.6 | c.686A>G | p.His229Arg | missense_variant | 3/3 | 1 | NM_206937.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00171 AC: 260AN: 152232Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000488 AC: 122AN: 250222Hom.: 0 AF XY: 0.000355 AC XY: 48AN XY: 135326
GnomAD4 exome AF: 0.000168 AC: 245AN: 1461032Hom.: 1 Cov.: 34 AF XY: 0.000139 AC XY: 101AN XY: 726844
GnomAD4 genome ? AF: 0.00171 AC: 260AN: 152350Hom.: 0 Cov.: 33 AF XY: 0.00172 AC XY: 128AN XY: 74508
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | May 04, 2015 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Mar 05, 2018 | - - |
DNA ligase IV deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
LIG4-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 09, 2020 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at