rs2074522
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_013975.4(LIG3):c.2675-39G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0971 in 1,598,088 control chromosomes in the GnomAD database, including 8,204 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.090 ( 690 hom., cov: 32)
Exomes 𝑓: 0.098 ( 7514 hom. )
Consequence
LIG3
NM_013975.4 intron
NM_013975.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.341
Genes affected
LIG3 (HGNC:6600): (DNA ligase 3) This gene is a member of the DNA ligase family. Each member of this family encodes a protein that catalyzes the joining of DNA ends but they each have a distinct role in DNA metabolism. The protein encoded by this gene is involved in excision repair and is located in both the mitochondria and nucleus, with translation initiation from the upstream start codon allowing for transport to the mitochondria and translation initiation from a downstream start codon allowing for transport to the nucleus. Additionally, alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LIG3 | NM_013975.4 | c.2675-39G>A | intron_variant | ENST00000378526.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LIG3 | ENST00000378526.9 | c.2675-39G>A | intron_variant | 1 | NM_013975.4 | P1 | |||
LIG3 | ENST00000262327.9 | c.2675-39G>A | intron_variant | 1 | |||||
LIG3 | ENST00000593099.5 | n.2528-39G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0902 AC: 13728AN: 152124Hom.: 691 Cov.: 32
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GnomAD3 exomes AF: 0.103 AC: 23446AN: 227626Hom.: 1344 AF XY: 0.108 AC XY: 13351AN XY: 123122
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GnomAD4 exome AF: 0.0979 AC: 141497AN: 1445846Hom.: 7514 Cov.: 31 AF XY: 0.100 AC XY: 71928AN XY: 718186
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GnomAD4 genome ? AF: 0.0901 AC: 13722AN: 152242Hom.: 690 Cov.: 32 AF XY: 0.0918 AC XY: 6835AN XY: 74436
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at