16-289499-C-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The NM_003502.4(AXIN1):c.2403G>A(p.Arg801Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00775 in 1,612,972 control chromosomes in the GnomAD database, including 66 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_003502.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AXIN1 | NM_003502.4 | c.2403G>A | p.Arg801Arg | synonymous_variant | Exon 10 of 11 | ENST00000262320.8 | NP_003493.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AXIN1 | ENST00000262320.8 | c.2403G>A | p.Arg801Arg | synonymous_variant | Exon 10 of 11 | 1 | NM_003502.4 | ENSP00000262320.3 | ||
AXIN1 | ENST00000354866.7 | c.2295G>A | p.Arg765Arg | synonymous_variant | Exon 9 of 10 | 1 | ENSP00000346935.3 | |||
AXIN1 | ENST00000457798.1 | c.156G>A | p.Arg52Arg | synonymous_variant | Exon 2 of 3 | 3 | ENSP00000416835.1 | |||
AXIN1 | ENST00000461023.5 | n.5472G>A | non_coding_transcript_exon_variant | Exon 7 of 8 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00512 AC: 780AN: 152214Hom.: 6 Cov.: 33
GnomAD3 exomes AF: 0.00517 AC: 1294AN: 250056Hom.: 11 AF XY: 0.00491 AC XY: 666AN XY: 135682
GnomAD4 exome AF: 0.00803 AC: 11725AN: 1460640Hom.: 60 Cov.: 33 AF XY: 0.00790 AC XY: 5738AN XY: 726618
GnomAD4 genome AF: 0.00512 AC: 780AN: 152332Hom.: 6 Cov.: 33 AF XY: 0.00462 AC XY: 344AN XY: 74484
ClinVar
Submissions by phenotype
not provided Benign:3
AXIN1: BP4, BP7, BS2 -
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Caudal duplication;C2239176:Hepatocellular carcinoma Benign:1
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AXIN1-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at