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JAK1
Final classification
VUS
PM2PP3
JAK1
c.1909G>A
p.Glu637Lys
This variant

NM_002227.3:c.1909G>A (p.Glu637Lys) is extremely rare in population databases, present in gnomAD v4.1 at an allele frequency of 1.24e-06 (2/1,613,736 alleles, 0 homozygotes) and absent from gnomAD v2.1 and gnomAD-Canada v1.0. This meets PM2 at the supporting level.

Transcript
NM_002227.3
HGVS · transcript:coding
NM_002227.3:c.1909G>A
GRCh38
chr1:64846727 C>T
GRCh37
chr1:65312410 C>T
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
JAK1 c.1909G>A

NM_002227.3:c.1909G>A (p.Glu637Lys) is extremely rare in population databases, present in gnomAD v4.1 at an allele frequency of 1.24e-06 (2/1,613,736 alleles, 0 homozygotes) and absent from gnomAD v2.1 and gnomAD-Canada v1.0. This meets PM2 at the supporting level.1 Computational evidence supports a deleterious effect: REVEL predicts a damaging score of 0.762, meeting PP3 at the supporting level under generic ACMG/AMP guidelines. SpliceAI predicts no splicing impact (max delta=0.00).2 This variant is a missense substitution (p.Glu637Lys) and does not meet PVS1 null-variant criteria. No functional studies, segregation data, de novo observations, case-control data, or prior clinical classifications are available. The variant has been reported in COSMIC (COSV61089427, n=2) in a somatic context but lacks germline disease association evidence.3 Only two supporting-level pathogenic criteria are met (PM2_supporting, PP3_supporting). No moderate, strong, or very strong pathogenic criteria are met. No benign criteria are met. Under generic ACMG/AMP 2015 combination rules (PMID:25741868), two supporting criteria are insufficient to reach Likely Pathogenic (minimum: 1 strong + 2 supporting, or 2 moderate + 2 supporting, or 3 moderate, etc.). The variant is classified as a Variant of Uncertain Significance (VUS).4

PM2 + PP3 VUS
2 revelspliceai ↗
3 pvs1_variant_assessmentclinvar ↗oncokb ↗
4 generic_acmg_combination_rules
Gene diagram · NM_002227.3 · variants mapped to exon structure
JAK1 NM_002227.3
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 19 assessed
MetEvidence satisfies this criterion.
Not metEvaluated against available evidence; threshold not reached.
Not assessedApplies in principle, but no evidence was found to evaluate it.
N/ADoesn't apply to this variant type.
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
NM_002227.3:c.1909G>A is extremely rare in population databases. It is absent from gnomAD v2.1 and present at very low frequency in gnomAD v4.1 (AF=1.24e-06, 2/1,613,736 alleles, 0 homozygotes). The highest subpopulation frequency is in the Remaining individuals group (AF=1.6e-05, 1/62,500 alleles). Absent from gnomAD-Canada v1.0. This allele frequency is well below the 0.1% PM2 threshold for a rare variant, supporting a moderately deleterious interpretation at the supporting level under generic ACMG/AMP.
gnomAD v2.1: absentgnomAD v4.1: AF=1.24e-06 (2/1613
PP3 supporting Pathogenic
Multiple lines of computational evidence support a deleterious effect. REVEL predicts a damaging score of 0.762 (above the 0.5 threshold commonly used for PP3_supporting). SpliceAI predicts no splice impact (max delta=0.00), which is expected for a missense substitution distant from splice junctions. BayesDel (0.268) is below typical deleterious thresholds, but REVEL, as an ensemble method incorporating multiple predictors, provides sufficient in silico support at the supporting level under generic ACMG/AMP.
REVEL score: 0.762 (deleterious prediction)BayesDel score: 0.268 (below typical deleterious threshold)SpliceAI max delta: 0.00 (no predicted splice impact)
Assessed · not applied · 4 not met · 15 not assessed
Pathogenic
PS1 No evidence was identified of a different nucleotide change at the same codon producing the same missense change (p.Glu637Lys).
PS2 No de novo data are available for NM_002227.3:c.1909G>A.
PS3 No well-established in vitro or in vivo functional studies were identified for NM_002227.3:c.1909G>A.
PS4 No case-control or prevalence data comparing affected individuals to general population controls are available for this variant.
PM1 This variant does not lie within a statistically significant mutational hotspot in JAK1.
PM6 No de novo data are available for NM_002227.3:c.1909G>A.
PP1 No co-segregation data are available for NM_002227.3:c.1909G>A.
PP2 Insufficient gene-level constraint data are available for JAK1 to determine whether missense variants are a common mechanism of disease with a low rate of benign missense variation.
PP4 No patient phenotype or clinical data are available for this case.
PP5 No reputable source has classified NM_002227.3:c.1909G>A as pathogenic.
Benign
BA1 The allele frequency of NM_002227.3:c.1909G>A (AF=1.24e-06 in gnomAD v4.1) is far below the 1% BA1 threshold.
BS1 The allele frequency of NM_002227.3:c.1909G>A (AF=1.24e-06, 0.00012%) is far below the 0.3% BS1 threshold.
BS2 No data are available regarding observation of NM_002227.3:c.1909G>A in healthy adults with full penetrance expected at an early age.
BS3 No well-established in vitro or in vivo functional studies demonstrating no deleterious effect of p.Glu637Lys are available.
BS4 No segregation data are available to assess lack of co-segregation with disease.
BP2 No data are available regarding observation of NM_002227.3:c.1909G>A in trans with a known pathogenic JAK1 variant.
BP4 Computational evidence does not support a benign interpretation.
BP5 No alternative molecular cause for disease has been identified in this case.
BP6 No reputable source has classified NM_002227.3:c.1909G>A as benign.
N/A · 4 PVS1 · PM5 · BP1 · 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= 1.23936e-06; MAF= 0.00012%, 2/1613736 alleles, homozygotes = 0) and has highest observed frequency in the Remaining individuals population (AF= 1.6e-05; MAF= 0.00160%, 1/62500 alleles, homozygotes = 0).
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
0.00012% · 2 / 1,613,736
0 hom
Remaining individuals
1 / 62,500
0.0016%
European (non-Finnish)
1 / 1,179,796
8.5e-05%
+ 8 not observed (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 = 0.762. BayesDel score = 0.267658.
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. JAK1, an intracellular kinase, is frequently altered in hematologic malignancies and gynecological 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 previously been reported in somatic cancers (COSMIC; COSV61089427, n = 2 times).
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