Starting
Initialising…
0%
Final classification
VUS
c.284_307delCCCCCGGACTCACACCACAGCCGC

NM_003016.4:c.284_307del is an in-frame deletion of 24 nucleotides in SRSF2, resulting in loss of 8 amino acids (p.Pro95_Arg102del) at the boundary of the RRM and RS-rich domains.

Gene
N/A
Transcript
N/A
HGVS · transcript:coding
NM_003016.4:c.284_307delCCCCCGGACTCACACCACAGCCGC
Consequence
N/A
GRCh38
N/A
GRCh37
N/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: PM4 moderate; combination = 1 moderate, 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: PM4 moderate; combination = 1 moderate, which maps to VUS.
Classification rationale
PM4 VUS
c.284_307delCCCCCGGACTCACACCACAGCCGC

NM_003016.4:c.284_307del is an in-frame deletion of 24 nucleotides in SRSF2, resulting in loss of 8 amino acids (p.Pro95_Arg102del) at the boundary of the RRM and RS-rich domains.1 The deletion meets PM4 (moderate) because it causes a protein length change through an in-frame deletion in a non-repetitive region, per ACMG/AMP 2015 guidelines.2 BP3 is not met because the deleted region is non-repetitive and includes Pro95, a residue of established functional significance in SRSF2.3 PVS1 is not applicable: the variant is an in-frame deletion rather than a null variant. Per ClinGen SVI PVS1 recommendations, in-frame deletions are not eligible for PVS1 at any strength level.4 Population frequency data from gnomAD v2.1 and v4.1 are unavailable due to incomplete variant normalization in the pipeline. gnomAD-Canada reports AC=0, AN=0 (no data), precluding application of PM2, BA1, or BS1. Pro95 is a known somatic mutational hotspot in SRSF2 (ClinVar: P95H Pathogenic, P95L Pathogenic, P95R Likely pathogenic), but germline hotspot evidence for SRSF2 is not established, so PM1 is not met in this context.5 Multiple criteria (PS2, PS3, PS4, PM6, PP1, PP4, BS2, BS3, BS4, BP2, BP5, BP6) remain not_assessed due to absence of case-level, functional, segregation, or population data in the available evidence. Based on available evidence, the only applicable criterion is PM4 (moderate). The evidence is insufficient to reach a definitive classification; the variant defaults to Variant of Uncertain Significance (VUS) under generic ACMG/AMP 2015 combination rules.6

PM4 VUS
2 generic_acmg_combination_rules
3 generic_acmg_combination_rules
5 generic_acmg_combination_rules
6 generic_acmg_combination_rules
Applied criteria · 1 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
      Population frequency
      This variant is absent from gnomAD v4.1.
      This variant is absent from gnomAD v2.1.
      This variant is absent from gnomAD-Canada.
      ClinVar No data
      No ClinVar submissions were recorded for this variant.
      In silico No data
      No in-silico prediction was recorded for this variant.
      Functional No data
      No calibrated functional assay or RNA evidence was identified for this variant.
      Somatic evidence
      COSMIC
      This variant has not previously been reported in somatic cancers (COSMIC).
      Hotspots
      This variant does not lie in a statistically significant cancer hotspot.
      Sources & reference links

      No sources recorded.