The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

  • No Criteria Specification was provided in the publication event for the variant classifaction.
  • The Criteria Specification shown below is a best-estimate based on the VCEP, gene, disease, and publication date.

Variant: NR_148928.1:n.1045T>C

CA281951

Gene: BRAF (HGNC:673)
Condition: RASopathy (MONDO:0021060)
Inheritance Mode: Autosomal dominant inheritance
UUID: 7808e324-29b8-43db-85ad-2f63caa01996
Approved on: 2019-05-10
Published on: 2019-06-28

HGVS expressions

NR_148928.1:n.1045T>C
NC_000007.14:g.140801532A>G
CM000669.2:g.140801532A>G
NC_000007.13:g.140501332A>G
CM000669.1:g.140501332A>G
NC_000007.12:g.140147801A>G
NG_007873.3:g.128233T>C
NM_004333.4:c.740T>C
NM_001354609.1:c.740T>C
NM_004333.5:c.740T>C
ENST00000288602.10:c.740T>C
ENST00000497784.1:n.775T>C
More

Likely Pathogenic

Met criteria codes 6
PP2 PP3 PM2 PM6 PM1 PS4_Supporting
Not Met criteria codes 17
BP7 BP5 BP1 BP4 BP2 BP3 BS1 BS4 BS3 BS2 PP1 PS2 PS3 PS1 BA1 PM4 PM5

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
RASopathy VCEP
The c.740T>C (p.Phe247Ser) variant in BRAF has been reported in the literature as an unconfirmed de novo occurrence in a patient with clinical features of a RASopathy (PM6, PS4_Supporting; GeneDx internal data; GTR Lab ID: 26957; NOT SUBMITTED TO CLINVAR YET). A different pathogenic missense variant has been previously identified at this codon of BRAF which may indicate that this residue is critical to the function of the protein (PM5 not applied due to PM1 application; ClinVar 55793, 180784). This variant was absent from large population studies (PM2; gnomAD, http://gnomad.broadinstitute.org). Furthermore, the variant is in a location that has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot or domain of BRAF (PM1; PMID 29493581). The variant is located in the BRAF gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). Computational prediction tools and conservation analysis suggest that the p.Phe247Ser variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as likely pathogenic for RASopathies in an autosomal dominant manner. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): PM6, PS4_Supporting, PM2, PM1, PP2, PP3.
Met criteria codes
PP2
Variant is in BRAF
PP3
REVEL score is 0.935
PM2
c.740T>C p.Phe247Ser variant is absent from gnomAD.
PM6
GeneDx: Variant was identified in patient with clinical features of RASopathy in an assumed de novo case
PM1
Variant is in exon 6 of BRAF
PS4_Supporting
GeneDx: Variant was identified in patient with clinical features of RASopathy. "Applied PP4"
Not Met criteria codes
BP7
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
p.Phe247Leu variant is Pathogenic, however PM1 has already been applied
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.
ClinGen Terms of Use.
¤ Powered by BCM's Genboree.