chr16-291218-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_003502.4(AXIN1):c.2266G>A(p.Val756Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000348 in 1,436,206 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003502.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AXIN1 | NM_003502.4 | c.2266G>A | p.Val756Met | missense_variant | 9/11 | ENST00000262320.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AXIN1 | ENST00000262320.8 | c.2266G>A | p.Val756Met | missense_variant | 9/11 | 1 | NM_003502.4 | A1 | |
AXIN1 | ENST00000354866.7 | c.2187-1611G>A | intron_variant | 1 | P4 | ||||
AXIN1 | ENST00000457798.1 | c.50-1611G>A | intron_variant | 3 | |||||
AXIN1 | ENST00000461023.5 | n.3753G>A | non_coding_transcript_exon_variant | 7/8 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome AF: 0.00000348 AC: 5AN: 1436206Hom.: 0 Cov.: 31 AF XY: 0.00000140 AC XY: 1AN XY: 712160
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 10, 2022 | The c.2266G>A (p.V756M) alteration is located in exon 9 (coding exon 8) of the AXIN1 gene. This alteration results from a G to A substitution at nucleotide position 2266, causing the valine (V) at amino acid position 756 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at