17-34986110-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_013975.4(LIG3):c.670C>T(p.Arg224Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000439 in 1,614,038 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R224L) has been classified as Uncertain significance.
Frequency
Consequence
NM_013975.4 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 | UniProt |
---|---|---|---|---|---|---|---|
LIG3 | NM_013975.4 | c.670C>T | p.Arg224Trp | missense_variant | 3/20 | ENST00000378526.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LIG3 | ENST00000378526.9 | c.670C>T | p.Arg224Trp | missense_variant | 3/20 | 1 | NM_013975.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000717 AC: 109AN: 152118Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00126 AC: 316AN: 251456Hom.: 1 AF XY: 0.00115 AC XY: 156AN XY: 135906
GnomAD4 exome AF: 0.000410 AC: 599AN: 1461802Hom.: 3 Cov.: 30 AF XY: 0.000382 AC XY: 278AN XY: 727206
GnomAD4 genome AF: 0.000723 AC: 110AN: 152236Hom.: 0 Cov.: 32 AF XY: 0.000994 AC XY: 74AN XY: 74426
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Oct 30, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at