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]
  • See Evidence submitted by expert panel for details.

Variant: NM_002880.3(RAF1):c.1108+9_1108+21delGGGGCCCTCCCTT

CA182757

178666 (ClinVar)

Gene: RAF1
Condition: RASopathy
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: e3caac03-d88a-45f8-bcde-e41975fe8745
Approved on: 2017-04-03
Published on: 2018-12-10

HGVS expressions

NM_002880.3:c.1108+9_1108+21del
NM_002880.3:c.1108+9_1108+21delGGGGCCCTCCCTT
NM_002880.3(RAF1):c.1108+9_1108+21delGGGGCCCTCCCTT
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
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
ENST00000251849.8:c.1108+9_1108+21del
ENST00000423275.5:c.*785+9_*785+21del
ENST00000432427.2:n.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
More

Benign

Met criteria codes 3
BA1 BP7 BP5

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
RASopathy VCEP
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). This variant is a synonymous (silent) variant at a nucleotide that is not highly conserved and is not predicted to impact splicing (BP7). The filtering allele frequency of the c.1108+9_1108+21del variant in the RAF1 gene is 0.0637% (54/66698) for European (Non-Finnish) chromosomes by the Exome Aggregation Consortium, which is a high enough frequency to be classified as benign based on thresholds defined by the ClinGen RASopathy Expert Panel for autosomal dominant RASopathy variants (BA1). In summary, this variant meets criteria to be classified as benign. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): BA1, BP5, BP7.
Met criteria codes
BA1
The filtering allele frequency of the c.1108+9_1108+21del variant in the RAF1 gene is 0.13% (17/8237) of European chromosomes by the NHLBI Exome Sequencing Project (ESP) Exome Variant Server, which is a high enough frequency to be classified as benign based on thresholds defined by the ClinGen RASopathy Expert Panel for autosomal dominant RASopathy variants (BA1).
BP7
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
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).
Curation History
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