rs13436
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_000234.3(LIG1):c.2442G>C(p.Ala814=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 1,611,088 control chromosomes in the GnomAD database, including 162,858 homozygotes. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. A814A) has been classified as Likely benign.
Frequency
Consequence
NM_000234.3 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LIG1 | NM_000234.3 | c.2442G>C | p.Ala814= | splice_region_variant, synonymous_variant | 26/28 | ENST00000263274.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LIG1 | ENST00000263274.12 | c.2442G>C | p.Ala814= | splice_region_variant, synonymous_variant | 26/28 | 1 | NM_000234.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.475 AC: 72135AN: 152012Hom.: 17560 Cov.: 34
GnomAD3 exomes AF: 0.463 AC: 113343AN: 244628Hom.: 27359 AF XY: 0.464 AC XY: 61256AN XY: 132114
GnomAD4 exome AF: 0.441 AC: 643367AN: 1458958Hom.: 145279 Cov.: 46 AF XY: 0.442 AC XY: 320384AN XY: 725416
GnomAD4 genome ? AF: 0.475 AC: 72196AN: 152130Hom.: 17579 Cov.: 34 AF XY: 0.475 AC XY: 35353AN XY: 74384
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Nov 12, 2023 | This variant is classified as Benign based on local population frequency. This variant was detected in 60% of patients studied by a panel of primary immunodeficiencies. Number of patients: 58. Only high quality variants are reported. - |
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 28, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at