Starting
Initialising…
0%
MITF
Final classification
VUS
MITF c.218G>A · p.Arg73His
MITF

NM_198159.3:c.218G>A (p.Arg73His) is a missense variant in MITF exon 2, classified under the generic ACMG/AMP 2015 framework as no CSPEC/VCEP framework is available for this gene.

Gene
MITF
Transcript
NM_198159.3
HGVS · transcript:coding
NM_198159.3:c.218G>A
Consequence
N/A
GRCh38
chr3:69879247 G>A
GRCh37
chr3:69928398 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, BP4 supporting benign; combination = 1 supporting + 1 supporting benign, 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, BP4 supporting benign; combination = 1 supporting + 1 supporting benign, which maps to VUS.
Classification rationale
PM2 BP4 VUS
MITF c.218G>A

NM_198159.3:c.218G>A (p.Arg73His) is a missense variant in MITF exon 2, classified under the generic ACMG/AMP 2015 framework as no CSPEC/VCEP framework is available for this gene. The variant is present at extremely low frequency in gnomAD: v2.1 AF = 0.0018% (5/280628 alleles) and v4.1 AF = 0.0032% (51/1614094 alleles), with no homozygotes observed. This meets PM2 at supporting level.1 Multiple lines of in silico evidence suggest a neutral effect: REVEL 0.285, BayesDel -0.025, and SpliceAI max delta 0.0, meeting BP4 at supporting benign level.2 No variant-specific functional studies, case-control analyses, de novo reports, cosegregation data, or expert panel classifications were identified for this variant. The variant has been reported in ClinVar as Uncertain Significance by two clinical laboratories.3 PVS1 is not applicable as the variant is missense. PM5 is not applicable as no pathogenic comparator exists at p.Arg73. BP1 is not applicable as MITF has known pathogenic missense variants. BP7 is not applicable as the variant is not synonymous. BP3, PM3, and PM4 were trivially not applicable per the assessment scope.4 With one supporting pathogenic criterion (PM2_Supporting) and one supporting benign criterion (BP4_Supporting), the evidence is balanced. The variant is classified as a Variant of Uncertain Significance (VUS) under the ACMG/AMP 2015 generic framework.5

PM2 + BP4 VUS
2 revelbayesdelspliceai ↗
4 pvs1_variant_assessmentpm5_candidates
5 generic_acmg_combination_rules
Gene diagram · NM_198159.3 · variants mapped to exon structure
MITF NM_198159.3
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
      Population frequency
      Overall AF
      51 / 1,614,094
      0.0032%
      Highest · Remaining individuals
      0.008%
      Homozygotes
      0
      grpmax FAF
      0.0027%
      Allele frequency by ancestry — gnomAD v4.1
      observed in 3 of 9 groups
      AncestryAllele countFrequencyHomozygotes
      European (non-Finnish) 42 / 1,180,054 0.0036% 0
      South Asian 3 / 91,094 0.0033% 0
      Admixed American 1 / 60,008 0.0017% 0
      European (Finnish) 0 / 64,030
      Amish 0 / 912
      East Asian 0 / 44,884
      Middle Eastern 0 / 6,084
      Ashkenazi Jewish 0 / 29,606
      African/African American 0 / 74,932
      This variant is present in gnomAD v4.1 (AF= 3.15967e-05; MAF= 0.00316%, 51/1614094 alleles, homozygotes = 0) and has highest observed frequency in the Remaining individuals population (AF= 8.00128e-05; MAF= 0.00800%, 5/62490 alleles, homozygotes = 0); grpmax FAF= 2.665e-05.
      Overall AF
      5 / 280,628
      0.0018%
      Highest · Remaining individuals
      0.014%
      Homozygotes
      0
      grpmax FAF
      0.00029%
      Allele frequency by ancestry — gnomAD v2.1
      observed in 3 of 8 groups
      AncestryAllele countFrequencyHomozygotes
      Remaining individuals 1 / 7,142 0.014% 0
      South Asian 1 / 30,602 0.0033% 0
      European (non-Finnish) 3 / 128,394 0.0023% 0
      African/African American 0 / 24,202
      Admixed American 0 / 35,370
      Ashkenazi Jewish 0 / 10,350
      East Asian 0 / 19,534
      European (Finnish) 0 / 25,034
      This variant is present in gnomAD v2.1 (AF= 1.78172e-05; MAF= 0.00178%, 5/280628 alleles, homozygotes = 0) and has highest observed frequency in the Remaining individuals population (AF= 0.000140017; MAF= 0.01400%, 1/7142 alleles, homozygotes = 0); grpmax FAF= 2.94e-06.
      This variant is absent from gnomAD-Canada.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Uncertain significance (2 clinical laboratories). (ClinVarID = 3377783)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.285. BayesDel score = -0.0249543.
      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. MITF, a transcription factor involved in melanocyte differentiation, is altered by mutation and amplification in melanomas.
      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 previously been reported in somatic cancers (COSMIC; COSV58891706, n = 3 times).
      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