rs3730933
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_000234.3(LIG1):āc.800A>Gā(p.Asn267Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0021 in 1,613,956 control chromosomes in the GnomAD database, including 62 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_000234.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LIG1 | NM_000234.3 | c.800A>G | p.Asn267Ser | missense_variant | 10/28 | ENST00000263274.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LIG1 | ENST00000263274.12 | c.800A>G | p.Asn267Ser | missense_variant | 10/28 | 1 | NM_000234.3 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0114 AC: 1730AN: 152066Hom.: 39 Cov.: 31
GnomAD3 exomes AF: 0.00300 AC: 754AN: 251496Hom.: 14 AF XY: 0.00210 AC XY: 286AN XY: 135922
GnomAD4 exome AF: 0.00113 AC: 1652AN: 1461772Hom.: 23 Cov.: 32 AF XY: 0.000968 AC XY: 704AN XY: 727214
GnomAD4 genome AF: 0.0114 AC: 1736AN: 152184Hom.: 39 Cov.: 31 AF XY: 0.0110 AC XY: 818AN XY: 74398
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at