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AXIN2
Final classification
VUS
AXIN2 c.1908-23C>T · p.?
AXIN2

NM_004655.4:c.1908-23C>T is a deep intronic variant in AXIN2 located 23 bp upstream of exon 7.

Gene
AXIN2
Transcript
NM_004655.4
HGVS · transcript:coding
NM_004655.4:c.1908-23C>T
Consequence
N/A
GRCh38
chr17:65536576 G>A
GRCh37
chr17:63532694 G>A
Basis gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 supporting; combination = 1 supporting, which maps to VUS.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 supporting; combination = 1 supporting, which maps to VUS.
Classification rationale
PM2 VUS
AXIN2 c.1908-23C>T

NM_004655.4:c.1908-23C>T is a deep intronic variant in AXIN2 located 23 bp upstream of exon 7. SpliceAI predicts no splicing impact for this variant (max delta score = 0.00), providing no computational evidence of altered splicing.1 The variant is present in gnomAD at extremely low frequency: v2.1 AF = 0.00109% (3/274,000 alleles) and v4.1 AF = 0.00037% (6/1,611,554 alleles), with no homozygotes observed (PM2_supporting). However, rarity alone is limited by the absence of a predicted functional consequence.2 This variant is absent from ClinVar, and no publications, functional studies, segregation data, or de novo observations are available.3 AXIN2 loss of function is a recognized germline disease mechanism associated with colorectal polyposis and tooth agenesis, but no variant-specific evidence exists to support pathogenicity of this deep intronic substitution.4 Based on the generic ACMG/AMP 2015 classification framework, the available evidence (PM2_supporting only) is insufficient to classify this variant as pathogenic or likely pathogenic. The variant is classified as a Variant of Uncertain Significance (VUS).5

PM2 VUS
4 pvs1_gene_context
5 generic_acmg_combination_rules
Gene diagram · NM_004655.4 · variants mapped to exon structure
AXIN2 NM_004655.4
Fetching transcript structure from UCSC…
Applied criteria · 1 applied · 16 assessed
Applied · 1
Strength Supporting Moderate Strong Very strong
PM2 supporting review Pathogenic
NM_004655.4:c.1908-23C>T is present in gnomAD at extremely low frequency: v2.1 AF = 0.00109% (3/274,000 alleles), v4.1 AF = 0.00037% (6/1,611,554 alleles), with no homozygotes observed. Both frequencies are well below the 0.1% PM2 threshold for dominant disorders. However, the variant is a deep intronic substitution with no predicted splicing impact (SpliceAI delta = 0.00), which limits the weight of population rarity as evidence of pathogenicity.
gnomAD v2.1 AF = 1.09e-05 (3/274000)v4.1 AF = 3.72e-06 (6/1
Assessed · not applied
Pathogenic
PS1 No known pathogenic variant has been reported at this nucleotide position (c.1908-23) in ClinVar or the literature.
PS2 No de novo observation has been reported for this variant.
PS3 No functional studies have been performed on NM_004655.4:c.1908-23C>T.
PS4 No case-control or statistical enrichment data are available for this variant.
PM1 NM_004655.4:c.1908-23C>T is located in intron 7, 23 bp upstream of the exon boundary.
PM6 No de novo observation has been reported for this variant.
PP1 No segregation data are available for this variant.
PP3 SpliceAI predicts no splicing impact (max delta score = 0.00).
PP4 No phenotype or clinical data are available for the individual(s) carrying this variant.
Benign
BA1 The highest observed population allele frequency is 0.00246% (NFE, gnomAD v2.1), which is well below the 1% BA1 threshold.
BS1 The highest observed population allele frequency is 0.00246% (NFE, gnomAD v2.1), which is well below the 0.3% BS1 threshold.
BS2 No data are available on observation of this variant in healthy adults for a fully penetrant dominant disorder.
BS3 No functional studies demonstrating no deleterious effect have been performed on this variant.
BS4 No segregation data are available.
BP2 No data available on co-occurrence with a known pathogenic variant.
BP4 SpliceAI predicts no splicing impact (max delta = 0.00) for this deep intronic variant.
N/A · 9 PVS1 · PM5 · PP2 · PP5 · BP1 · BP3 · BP5 · BP6 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
This variant is present in gnomAD v4.1 (AF= 3.72311e-06; MAF= 0.00037%, 6/1611554 alleles, homozygotes = 0) and has highest observed frequency in the Remaining individuals population (AF= 1.60251e-05; MAF= 0.00160%, 1/62402 alleles, homozygotes = 0); grpmax FAF= 1.24e-06.
v2.1
This variant is present in gnomAD v2.1 (AF= 1.09489e-05; MAF= 0.00109%, 3/274000 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 2.46285e-05; MAF= 0.00246%, 3/121810 alleles, homozygotes = 0); grpmax FAF= 3.12e-06.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.00037% · 6 / 1,611,554
0 hom · FAF 0.00012%
Remaining individuals
1 / 62,402
0.0016%
European (non-Finnish)
5 / 1,178,300
0.00042%
+ 8 not observed (Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
gnomAD v2.1
0.0011% · 3 / 274,000
0 hom · FAF 0.00031%
European (non-Finnish)
3 / 121,810
0.0025%
+ 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals, South Asian)
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
ClinVar screenshot
ClinVar
This variant is absent from ClinVar.
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
Functional No data
No calibrated functional assay or RNA evidence was identified for this variant.
OncoKB ↗
COSMIC screenshot
COSMIC
Somatic evidence
COSMIC
This variant has not previously been reported in somatic cancers (COSMIC).
Hotspots
This variant does not lie in a statistically significant cancer hotspot.
COSMIC ↗
Sources & reference links
7Sources
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC