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SH2B3
Final classification
VUS
SH2B3 c.419G>C · p.Arg140Pro
SH2B3

NM_005475.2:c.419G>C (p.Arg140Pro) is a missense variant in SH2B3 exon 2 that is absent from ClinVar and present at extremely low frequency in gnomAD v4.1 (3/1,472,034 alleles; AF=0.00020%).

Gene
SH2B3
Transcript
NM_005475.2
HGVS · transcript:coding
NM_005475.2:c.419G>C
Consequence
N/A
GRCh38
chr12:111418564 G>C
GRCh37
chr12:111856368 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, 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
SH2B3 c.419G>C

NM_005475.2:c.419G>C (p.Arg140Pro) is a missense variant in SH2B3 exon 2 that is absent from ClinVar and present at extremely low frequency in gnomAD v4.1 (3/1,472,034 alleles; AF=0.00020%).1 PM2 (supporting) is met: the variant is at extremely low population frequency, well below the 0.1% threshold.2 BP4 (supporting benign) is met: concordant in silico predictions from REVEL (0.165) and BayesDel (-0.347) indicate a benign effect, and SpliceAI predicts no splice alteration (max delta 0.00).3 PVS1 is not applicable as this is a missense variant that does not fall into any null-variant category per ClinGen SVI PVS1 recommendations.4 No pathogenic or benign criteria beyond PM2 and BP4 are met. No variant-specific functional data, clinical observations, de novo events, segregation data, or literature reports exist for this variant. With one supporting pathogenic criterion (PM2) and one supporting benign criterion (BP4), the evidence is balanced with a slight lean toward uncertain significance given the absence of any functional or clinical data.5

PM2 + BP4 VUS
3 revelbayesdelspliceai ↗
4 pvs1_generic_framework ↗pvs1_variant_assessment
5 generic_acmg_combination_rules
Gene diagram · NM_005475.2 · variants mapped to exon structure
SH2B3 NM_005475.2
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 21 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
NM_005475.2:c.419G>C is absent from gnomAD v2.1 and is present at extremely low frequency in gnomAD v4.1 (3/1,472,034 alleles; AF=0.00020%), well below the 0.1% threshold for PM2. No homozygotes observed. The variant is absent from gnomAD-Canada v1.0.
gnomAD v2.1: absentgnomAD v4.1: AF=2.038e-06 (0.00020%)3/1
BP4 supporting Benign
Multiple lines of computational evidence suggest no impact on the gene product. REVEL score is 0.165 (below the 0.5 pathogenic threshold, predicting benign). BayesDel score is -0.347 (negative score predicts benign). SpliceAI delta score is 0.00 (no predicted splice impact). These concordant benign predictions from independent in silico tools support BP4 at supporting benign strength.
REVEL: 0.165 (benign)BayesDel: -0.347 (benign)SpliceAI: max delta 0.00 (no splice effect)
Assessed · not applied
Pathogenic
PS1 No alternate nucleotide change at codon 140 producing the same Arg140Pro missense change has been reported as pathogenic.
PS2 No de novo observation has been reported for NM_005475.2:c.419G>C.
PS3 No variant-specific functional studies have been reported for NM_005475.2:c.419G>C (p.Arg140Pro).
PS4 No case-control or cohort prevalence data exist for this variant.
PM1 Residue 140 does not lie within a statistically significant mutational hotspot per cancerhotspots.org.
PM5 No pathogenic missense variant at codon 140 has been identified in ClinVar or other databases.
PM6 No de novo observation has been reported for this variant.
PP1 No cosegregation data is available for this variant.
PP2 Insufficient data to evaluate whether SH2B3 has a low rate of benign missense variation and whether missense variants are a common disease mechanism.
PP3 Multiple in silico tools predict a benign effect.
PP4 No patient phenotype data is available for this variant.
PP5 No reputable source has reported this variant as pathogenic.
Benign
BA1 The overall allele frequency in gnomAD v4.1 is 0.00020% (AF=2.038e-06), well below the BA1 threshold of >1%.
BS1 The allele frequency in gnomAD v4.1 is 0.00020%, below the BS1 threshold of >0.3%.
BS2 No homozygous individuals are observed in gnomAD v4.1 (0/1,472,034 alleles).
BS3 No well-established in vitro or in vivo functional studies demonstrate no damaging effect on the SH2B3 gene product for this variant.
BS4 No segregation data is available for this variant.
BP1 While this is a missense variant, loss of function is an established disease mechanism for SH2B3 based on germline literature supporting biallelic SH2B3 alterations in hematopoietic disorders.
BP2 No data regarding observation in trans with a known pathogenic variant is available.
BP5 No alternate molecular basis for disease has been identified in an individual harboring this variant.
BP6 No reputable source has reported this variant as benign.
N/A · 2 PVS1 · 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= 2.038e-06; MAF= 0.00020%, 3/1472034 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 2.685e-06; MAF= 0.00027%, 3/1117320 alleles, homozygotes = 0); grpmax FAF= 7.2e-07.
v2.1
Absent from gnomAD v2.1.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.0002% · 3 / 1,472,034
0 hom · FAF 7.2e-05%
European (non-Finnish)
3 / 1,117,320
0.00027%
+ 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
gnomAD v2.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
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). REVEL score = 0.165. BayesDel score = -0.347111.
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. SH2B3 is an adaptor protein that regulates growth factor and cytokine signaling. Mutations are found in hematopoietic disorders including leukemias an
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