The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computer assertion could be determined for this classification!


Variant: NM_001754.5(RUNX1):c.98-20_98-18del

CA658799414

517187 (ClinVar)

Gene: RUNX1
Condition: hereditary thrombocytopenia and hematologic cancer predisposition syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: a25c99de-f2c1-46a5-a581-84790919971a
Approved on: 2024-08-12
Published on: 2024-08-12

HGVS expressions

NM_001754.5:c.98-20_98-18del
NM_001754.5(RUNX1):c.98-20_98-18del
NC_000021.9:g.34887118_34887120del
CM000683.2:g.34887118_34887120del
NC_000021.8:g.36259415_36259417del
CM000683.1:g.36259415_36259417del
NC_000021.7:g.35181285_35181287del
NG_011402.2:g.1102596_1102598del
ENST00000675419.1:c.98-20_98-18del
ENST00000300305.7:c.98-20_98-18del
ENST00000344691.8:c.-4_-2del
ENST00000358356.9:c.-4_-2del
ENST00000399237.6:c.62-20_62-18del
ENST00000399240.5:c.-4_-2del
ENST00000437180.5:c.98-20_98-18del
ENST00000455571.5:c.59-20_59-18del
ENST00000475045.6:c.98-20_98-18del
ENST00000482318.5:c.59-6403_59-6401del
NM_001001890.2:c.-4_-2del
NM_001122607.1:c.-4_-2del
NM_001754.4:c.98-20_98-18del
NM_001001890.3:c.-4_-2del
NM_001122607.2:c.-4_-2del
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Uncertain Significance

Met criteria codes 2
PM2_Supporting BP4
Not Met criteria codes 24
BA1 BS2 BS4 BS3 BS1 BP2 BP3 BP1 PVS1 BP7 BP5 PS2 PS4 PS3 PS1 PP1 PP4 PP3 PP2 PM1 PM5 PM3 PM4 PM6

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Myeloid Malignancy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 2

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Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Myeloid Malignancy VCEP
NM_001754.5(RUNX1):c.98-20_98-18del is an intronic variant which has a SpliceAI Δ score ≤ 0.20 (0.00 except for 0.05 at acceptor gain) (BP4). It is completely absent from all population databases (gnomAD v2.1.1, gnomAD v3.1.2, and ExAC v1.0) with at least 20x coverage for RUNX1 (PM2_Supporting). In summary, the clinical significance of this variant is uncertain. ACMG/AMP criteria applied, as specified by the Myeloid Malignancy Variant Curation Expert Panel for RUNX1: BP4, PM2_Supporting.
Met criteria codes
PM2_Supporting
This variant is completely absent from all population databases (gnomAD v2.1.1, gnomAD v3.1.2 and ExAC v1.0) with at least 20X coverage for RUNX1 (PM2_Supporting).
BP4
This intronic variant has a SpliceAI Δ score ≤0.20 (0.00 except for 0.05 at acceptor gain) (BP4).
Not Met criteria codes
BA1
This variant is completely absent from all population databases (gnomAD v2.1.1, gnomAD v3.1.2 and ExAC v1.0) with at least 20X coverage for RUNX1.
BS2
This rule is not applicable for MM-VCEP.
BS4
No reported cases of this variant identified.
BS3
No functional studies of this variant identified.
BS1
This variant is completely absent from all population databases (gnomAD v2.1.1, gnomAD v3.1.2 and ExAC v1.0) with at least 20X coverage for RUNX1.
BP2
No reported cases of this variant identified.
BP3
This rule is not applicable for MM-VCEP.
BP1
This rule is not applicable for MM-VCEP.
PVS1
This intronic variant is not predicted to cause any loss of function.
BP7
This intronic variant has a SpliceAI Δ score ≤0.20 (0.00 except for 0.05 at acceptor gain) BUT It has a PhloP score of >2.0 (PhloP score ranged from 6.81254 to 8.05383 across the 3 nucleotides as per USCS) and these 3 nucleotides were conserved across primates and mammals.
BP5
This rule is not applicable for MM-VCEP.
PS2
No reported cases of this variant identified.
PS4
No reported cases of this variant identified.
PS3
No functional studies of this variant identified.
PS1
This is an intronic variant not predicted to result in an amino acid change.
PP1
No reported cases of this variant identified.
PP4
This rule is not applicable for MM-VCEP.
PP3
This intronic variant has a SpliceAI Δ score ≤0.20 (0.00 except for 0.05 at acceptor gain).
PP2
This rule is not applicable for MM-VCEP.
PM1
This variant is not within the RHD as specified by MM-VCEP.
PM5
This is an intronic variant not predicted to result in an amino acid change.
PM3
This rule is not applicable for MM-VCEP.
PM4
This variant is not predicted to impact protein length.
PM6
No reported cases of this variant identified.
Curation History
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