13-108211243-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_206937.2(LIG4):c.26C>T(p.Thr9Ile) variant causes a missense change. The variant allele was found at a frequency of 0.165 in 1,610,136 control chromosomes in the GnomAD database, including 23,469 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_206937.2 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 rank | MANE | Protein | UniProt |
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LIG4 | NM_206937.2 | c.26C>T | p.Thr9Ile | missense_variant | Exon 3 of 3 | ENST00000442234.6 | NP_996820.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.163 AC: 24709AN: 151982Hom.: 2250 Cov.: 32
GnomAD3 exomes AF: 0.177 AC: 43666AN: 247176Hom.: 4384 AF XY: 0.170 AC XY: 22884AN XY: 134540
GnomAD4 exome AF: 0.165 AC: 240295AN: 1458036Hom.: 21217 Cov.: 34 AF XY: 0.162 AC XY: 117597AN XY: 725348
GnomAD4 genome AF: 0.163 AC: 24721AN: 152100Hom.: 2252 Cov.: 32 AF XY: 0.168 AC XY: 12458AN XY: 74332
ClinVar
Submissions by phenotype
not specified Benign:6
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, Clinvar assertions are benign and protective (not pathogenic) -
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This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
This variant is classified as Benign based on local population frequency. This variant was detected in 39% of patients studied by a panel of primary immunodeficiencies. Number of patients: 37. Only high quality variants are reported. -
DNA ligase IV deficiency Benign:3
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This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. -
not provided Benign:2Other:1
Variant interpreted as Benign and reported on 04-27-2020 by Lab or GTR ID 500031. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. This variant was reported in an individual referred for clinical diagnostic genetic testing. -
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Multiple myeloma, resistance to Benign:1
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Severe combined immunodeficiency due to DCLRE1C deficiency Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at