Starting
Initialising…
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B3GALT6
Final classification
VUS
B3GALT6 c.902_905dup · p.Glu303AlafsTer141
B3GALT6

NM_080605.4:c.902_905dup is a 4bp duplication producing a frameshift predicted to yield NP_542172.2:p.(Glu303AlafsTer141) in B3GALT6, a gene where loss of function is an established disease mechanism for autosomal recessive Ehlers-Danlos-syndrome-like connective tissue disorder (PVS1_Moderate; PMID:23664118, PMC6185798). The NM_080605.4 transcript is MANE Select and represents the single exon of B3GALT6; nonsense-mediated decay is not expected, warranting a downgrade from PVS1_VeryStrong to PVS1_Moderate per ClinGen SVI PVS1 recommendations.

Gene
B3GALT6
Transcript
NM_080605.4
HGVS · transcript:coding
NM_080605.4:c.902_905dup
Consequence
N/A
GRCh38
chr1:1233179 A>AAGCG
GRCh37
chr1:1168559 A>AAGCG
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: PVS1 moderate, PM2 moderate; combination = 2 moderate, 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: PVS1 moderate, PM2 moderate; combination = 2 moderate, which maps to VUS.
Classification rationale
PVS1PM2 VUS
B3GALT6 c.902_905dup

NM_080605.4:c.902_905dup is a 4bp duplication producing a frameshift predicted to yield NP_542172.2:p.(Glu303AlafsTer141) in B3GALT6, a gene where loss of function is an established disease mechanism for autosomal recessive Ehlers-Danlos-syndrome-like connective tissue disorder (PVS1_Moderate; PMID:23664118, PMC6185798). The NM_080605.4 transcript is MANE Select and represents the single exon of B3GALT6; nonsense-mediated decay is not expected, warranting a downgrade from PVS1_VeryStrong to PVS1_Moderate per ClinGen SVI PVS1 recommendations.1 This variant is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0 population databases (allele frequency = 0.0 in all datasets), meeting PM2 for extremely low population frequency.2 Combining the above, two moderate-level pathogenic criteria (PVS1_Moderate + PM2_Moderate) are insufficient to reach a Likely Pathogenic classification under generic ACMG/AMP 2015 combination rules (PMID:25741868), which require at minimum one Very Strong plus one Moderate, one Strong plus one Moderate, or three Moderate criteria. No benign criteria are met. The variant is classified as a Variant of Uncertain Significance (VUS).3

PVS1 + PM2 VUS
3 generic_acmg_combination_rules
Gene diagram · NM_080605.4 · variants mapped to exon structure
B3GALT6 NM_080605.4
Fetching transcript structure from UCSC…
Applied criteria · 2 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      Research & evidence
      Population frequency
      gnomAD v4.1 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      Population frequency
      Absent from gnomAD v4.1.
      Absent from gnomAD v2.1.
      This variant is absent from gnomAD-Canada.
      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 = 0.02).
      Functional No data
      No calibrated functional assay or RNA evidence was identified for this variant.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      Cancer hotspots
      Somatic evidence Not in COSMIC / hotspots
      COSMIC
      This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
      Hotspots
      This variant does not lie in a statistically significant hotspot.
      Sources & reference links
      7Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots