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ZRSR2
Final classification
VUS
ZRSR2 c.758T>C · p.Val253Ala
ZRSR2

NM_005089.3:c.758T>C (p.Val253Ala) is a missense variant in ZRSR2, a gene encoding a component of the minor spliceosome that is implicated in myelodysplastic syndromes, spliceosomopathies, and oral-facial-digital syndrome.

Gene
ZRSR2
Transcript
NM_005089.3
HGVS · transcript:coding
NM_005089.3:c.758T>C
Consequence
N/A
GRCh38
chrX:15815877 T>C
GRCh37
chrX:15834000 T>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; combination = 1 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; combination = 1 supporting, which maps to VUS.
Classification rationale
PM2 VUS
ZRSR2 c.758T>C

NM_005089.3:c.758T>C (p.Val253Ala) is a missense variant in ZRSR2, a gene encoding a component of the minor spliceosome that is implicated in myelodysplastic syndromes, spliceosomopathies, and oral-facial-digital syndrome.1 The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada population databases, meeting PM2 at supporting level.2 The variant is absent from ClinVar, COSMIC, and CancerHotspots.org; no variant-specific functional data, segregation data, or de novo observations are available.3 SpliceAI predicts no significant splicing impact (max delta score 0.04). BayesDel add score is 0.527 (above the 0.27 damaging threshold), but as the sole predictor available, it does not meet the PP3 multiple-lines requirement.4 No publications in the literature packet mention the specific variant NM_005089.3:c.758T>C (p.Val253Ala). Five PMIDs reviewed for ZRSR2 gene-level context did not contain variant-specific data. PVS1 is not applicable as this is a missense variant not falling into the null-variant buckets of the ClinGen PVS1 decision framework (PMC6185798).5 Overall classification is limited by paucity of evidence. Only one supporting-level criterion (PM2) is met, which is insufficient to reach a Likely Pathogenic or Pathogenic classification under generic ACMG/AMP 2015 combination rules. No benign criteria are met.6

PM2 VUS
1 pvs1_gene_context
4 spliceai ↗bayesdel
5 pvs1_generic_framework ↗pvs1_variant_assessment
6 generic_acmg_combination_rules
Gene diagram · NM_005089.3 · variants mapped to exon structure
ZRSR2 NM_005089.3
Fetching transcript structure from UCSC…
Applied criteria · 1 applied · 20 assessed
Applied · 1
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
NM_005089.3:c.758T>C is absent from gnomAD v2.1 (exomes), gnomAD v4.1 (exomes), and gnomAD-Canada v1.0 (genomes). The variant allele frequency is well below the 0.1% threshold for PM2 application in a gene without a CSPEC-specific frequency cutoff.
Absent from gnomAD v2.1 (exomes).Absent from gnomAD v4.1 (exomes).Absent from gnomAD-Canada v1.0 (HostSeq genomes).
Assessed · not applied
Pathogenic
PS2 No de novo confirmation data are available for this variant.
PS3 No variant-specific functional data exist for NM_005089.3:c.758T>C (p.Val253Ala).
PS4 No case-control or cohort data demonstrating statistically significant enrichment of this variant in affected individuals versus controls are available.
PM1 Residue 253 does not lie in a statistically significant cancer hotspot per CancerHotspots.org.
PM6 No de novo observation reported for this variant.
PP1 No segregation data are available for this variant.
PP2 ZRSR2 does not have an HCI prior score or externally calculated missense constraint metric available.
PP3 PP3 requires multiple lines of computational evidence supporting a deleterious effect.
PP4 No patient phenotype or family history data are available for adjudication.
PP5 This variant is absent from ClinVar.
Benign
BA1 The variant is absent from all gnomAD datasets.
BS1 The variant is absent from all gnomAD datasets.
BS2 No observation of this variant in healthy adult controls beyond population databases is available.
BS3 No well-established in vitro or in vivo functional studies demonstrate a benign effect for this variant.
BS4 No family segregation or linkage data are available to demonstrate lack of segregation with disease.
BP1 BP1 applies when a missense variant occurs in a gene for which primarily truncating variants cause disease.
BP2 BP2 requires observation of the variant in trans with a pathogenic variant for a fully penetrant dominant disorder, or in cis with a pathogenic variant in a recessive disorder.
BP4 BP4 requires multiple lines of computational evidence suggesting no impact on gene or gene product.
BP5 No observation of this variant in a case with an alternate molecular basis for disease is available.
BP6 This variant is absent from ClinVar.
N/A · 7 PVS1 · PS1 · PM3 · PM4 · PM5 · BP3 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
Absent from gnomAD v4.1.
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
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
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 = 0.04). BayesDel score = 0.527207.
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. ZRSR2, a splicing factor, is altered in various hematological malignancies.
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