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DDR2
Final classification
VUS
DDR2 c.1723G>C · p.Gly575Arg
DDR2

NM_006182.3:c.1723G>C (p.Gly575Arg) is a missense variant in exon 13 of DDR2. It is extremely rare in population databases, with a global allele frequency of 1.42e-05 in gnomAD v2.1 (4/282,340 alleles) and 5.58e-06 in gnomAD v4.1 (9/1,614,004 alleles), meeting PM2 at supporting strength.

Gene
DDR2
Transcript
NM_006182.3
HGVS · transcript:coding
NM_006182.3:c.1723G>C
Consequence
N/A
GRCh38
chr1:162772242 G>C
GRCh37
chr1:162742032 G>C
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, PP3 supporting; combination = 2 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, PP3 supporting; combination = 2 supporting, which maps to VUS.
Classification rationale
PM2PP3 VUS
DDR2 c.1723G>C

NM_006182.3:c.1723G>C (p.Gly575Arg) is a missense variant in exon 13 of DDR2. It is extremely rare in population databases, with a global allele frequency of 1.42e-05 in gnomAD v2.1 (4/282,340 alleles) and 5.58e-06 in gnomAD v4.1 (9/1,614,004 alleles), meeting PM2 at supporting strength.1 REVEL predicts a deleterious score of 0.972, meeting PP3 at supporting strength. BayesDel (0.558) is consistent with this prediction. SpliceAI predicts no splicing impact (max delta = 0.00).2 This variant has been reported in ClinVar as Uncertain significance by a single clinical laboratory (Labcorp Genetics, variation ID 4701000). No functional studies, segregation data, de novo observations, or case-control data are available for this variant.3 PVS1 is not applicable as this is a missense variant; PM5 is not applicable as no pathogenic missense variant at the same residue has been identified; BP7 is not applicable as this is not a synonymous variant.4

PM2 + PP3 VUS
Gene diagram · NM_006182.3 · variants mapped to exon structure
DDR2 NM_006182.3
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
      v4.1
      This variant is present in gnomAD v4.1 (AF= 5.57619e-06; MAF= 0.00056%, 9/1614004 alleles, homozygotes = 0) and has highest observed frequency in the Admixed American population (AF= 5.0005e-05; MAF= 0.00500%, 3/59994 alleles, homozygotes = 0); grpmax FAF= 1.327e-05.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 1.41673e-05; MAF= 0.00142%, 4/282340 alleles, homozygotes = 0) and has highest observed frequency in the Admixed American population (AF= 5.65195e-05; MAF= 0.00565%, 2/35386 alleles, homozygotes = 0); grpmax FAF= 9.59e-06.
      🇨🇦 CA
      Not available in gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.00056% · 9 / 1,614,004
      0 hom · FAF 0.0013%
      Admixed American
      3 / 59,994
      0.005%
      Remaining individuals
      1 / 62,484
      0.0016%
      European (non-Finnish)
      5 / 1,180,018
      0.00042%
      + 7 not observed (European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
      gnomAD v2.1
      0.0014% · 4 / 282,340
      0 hom · FAF 0.00096%
      Admixed American
      2 / 35,386
      0.0057%
      European (non-Finnish)
      2 / 128,832
      0.0016%
      + 6 not observed (African/African 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 has been reported in ClinVar as Uncertain significance (1 clinical laboratory). (ClinVarID = 4701000)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.972. BayesDel score = 0.558463.
      Functional / OncoKB screenshot
      Functional Unknown Oncogenic Effect
      OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. DDR2, a receptor tyrosine kinase, is mutated at low frequencies in various cancers.
      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
      8Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots