Evidence Repository
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 label mismatch: RAF1 vs undefined
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!

Variant: NM_002880.4(RAF1):c.1108+9_1108+21del

CA182757

178666 (ClinVar)

Gene: RAF1
Condition: RASopathy
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: e3caac03-d88a-45f8-bcde-e41975fe8745
Approved on: 2024-12-03
Published on: 2025-03-25

HGVS expressions

NM_002880.4:c.1108+9_1108+21del
NM_002880.4(RAF1):c.1108+9_1108+21del
NC_000003.12:g.12599673_12599685del
CM000665.2:g.12599673_12599685del
NC_000003.11:g.12641172_12641184del
CM000665.1:g.12641172_12641184del
NC_000003.10:g.12616172_12616184del
NG_007467.1:g.69498_69510del
ENST00000423275.6:c.*773+9_*773+21del
ENST00000432427.3:c.428+9_428+21del
ENST00000465826.6:n.699+9_699+21del
ENST00000491290.2:n.1485+9_1485+21del
ENST00000684903.1:c.*785+9_*785+21del
ENST00000685348.1:c.*785+9_*785+21del
ENST00000685437.1:c.1009+9_1009+21del
ENST00000685653.1:c.1108+9_1108+21del
ENST00000685738.1:c.1108+9_1108+21del
ENST00000686409.1:n.2159+9_2159+21del
ENST00000686455.1:n.1471+9_1471+21del
ENST00000686479.1:n.1488_1500del
ENST00000686762.1:c.1108+9_1108+21del
ENST00000687257.1:n.1344+9_1344+21del
ENST00000687326.1:c.1108+9_1108+21del
ENST00000687486.1:c.300+9_300+21del
ENST00000687505.1:n.1226+9_1226+21del
ENST00000687923.1:c.997+21_997+33del
ENST00000687940.1:n.1485+9_1485+21del
ENST00000688269.1:n.1704+9_1704+21del
ENST00000688326.1:c.428+9_428+21del
ENST00000688444.1:n.1434+9_1434+21del
ENST00000688543.1:c.1009+9_1009+21del
ENST00000688625.1:c.*686+9_*686+21del
ENST00000688803.1:n.1339+9_1339+21del
ENST00000688914.1:n.94+9_94+21del
ENST00000689097.1:c.*785+9_*785+21del
ENST00000689389.1:c.1108+9_1108+21del
ENST00000689418.1:c.*785+9_*785+21del
ENST00000689481.1:c.*785+9_*785+21del
ENST00000689540.1:n.1258+9_1258+21del
ENST00000689876.1:c.1108+9_1108+21del
ENST00000689914.1:c.1108+9_1108+21del
ENST00000690397.1:c.997+9_997+21del
ENST00000690460.1:c.1096+9_1096+21del
ENST00000690625.1:n.1411+9_1411+21del
ENST00000691396.1:c.*901+9_*901+21del
ENST00000691724.1:c.*65+9_*65+21del
ENST00000691779.1:c.*686+9_*686+21del
ENST00000691899.1:c.1108+9_1108+21del
ENST00000692069.1:n.1674+9_1674+21del
ENST00000692093.1:c.1009+9_1009+21del
ENST00000692311.1:n.1932+9_1932+21del
ENST00000692558.1:n.1473+9_1473+21del
ENST00000692773.1:c.*845+9_*845+21del
ENST00000692830.1:c.*853+9_*853+21del
ENST00000693069.1:c.1009+9_1009+21del
ENST00000693312.1:c.883+9_883+21del
ENST00000693664.1:c.1108+9_1108+21del
ENST00000693705.1:c.*785+9_*785+21del
ENST00000251849.9:c.1108+9_1108+21del
ENST00000442415.7:c.1168+9_1168+21del
ENST00000251849.8:c.1108+9_1108+21del
ENST00000423275.5:c.*785+9_*785+21del
ENST00000432427.2:c.745+9_745+21del
ENST00000442415.6:c.1168+9_1168+21del
ENST00000460610.1:n.65+9_65+21del
ENST00000465826.5:n.352+9_352+21del
NM_002880.3:c.1108+9_1108+21del
NM_001354689.1:c.1168+9_1168+21del
NM_001354690.1:c.1108+9_1108+21del
NM_001354691.1:c.865+9_865+21del
NM_001354692.1:c.865+9_865+21del
NM_001354693.1:c.1009+9_1009+21del
NM_001354694.1:c.925+9_925+21del
NM_001354695.1:c.766+9_766+21del
NR_148940.1:n.1523+9_1523+21del
NR_148941.1:n.1523+9_1523+21del
NR_148942.1:n.1521+9_1521+21del
NM_001354689.3:c.1168+9_1168+21del
NM_001354690.2:c.1108+9_1108+21del
NM_001354691.2:c.865+9_865+21del
NM_001354692.2:c.865+9_865+21del
NM_001354693.2:c.1009+9_1009+21del
NM_001354694.2:c.925+9_925+21del
NM_001354695.2:c.766+9_766+21del
NR_148940.2:n.1439+9_1439+21del
NR_148941.2:n.1439+9_1439+21del
NR_148942.2:n.1437+9_1437+21del
NM_001354690.3:c.1108+9_1108+21del
NM_001354691.3:c.865+9_865+21del
NM_001354692.3:c.865+9_865+21del
NM_001354693.3:c.1009+9_1009+21del
NM_001354694.3:c.925+9_925+21del
NM_001354695.3:c.766+9_766+21del
NR_148940.3:n.1439+9_1439+21del
NR_148941.3:n.1439+9_1439+21del
NR_148942.3:n.1437+9_1437+21del
More

Benign

Met criteria codes 3
BA1 BP5 BP7

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for RAF1 Version 2.3.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
RASopathy VCEP
The c.1108+9_1108+21del variant is located in intron 10 of the RAF1 gene. This variant has a filtering allele frequency of 0.05951% in the European (non-Finnish) population in gnomAD v2, which is higher than the ClinGen RASopathy VCEP threshold (>0.0005) for BA1 and therefore meets this criterion (BA1). The variant is a synonymous (silent) variant at a nucleotide that is not highly conserved and is not predicted to impact splicing (BP7). Additionally, this variant has been identified in a patient with an alternate molecular basis for disease (BP5; GeneDx, Partners LMM internal data; GTR Lab ID's: 26957, 21766; ClinVar SCV000205113.4, SCV000209007.2). In summary, this variant meets criteria to be classified as benign for autosomal dominant RASopathies based on the ACMG/AMP criteria applied, as specified by the ClinGen RASopathy Variant Curation Expert Panel: BA1, BP5, BP7. (Specification Version 2.3, 12/3/2024)
Met criteria codes
BA1
This variant has a filtering allele frequency of 0.08037% in the European (non-Finnish) population in gnomAD v4, which is higher than the ClinGen RASopathy VCEP threshold (>0.0005) for BA1
BP5
The c.1108+9_1108+21del variant in the RAF1 gene has been identified in a patient with an alternate molecular basis for disease (BP5; GeneDx, Partners LMM internal data; GTR Lab ID's: 26957, 21766; ClinVar SCV000205113.4, SCV000209007.2).
BP7
The variant is not predicted by SpliceAI to impact splicing
Curation History
The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have questions about the information contained on this website, please see a health care professional.
¤ Powered by BCM's Genboree.