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

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Variant: NM_004333.6(BRAF):c.722C>A (p.Thr241Lys)

CA261663

44829 (ClinVar)

Gene: BRAF
Condition: RASopathy
Inheritance Mode: Autosomal dominant inheritance
UUID: 096bf007-b1b2-467c-a7b2-e9fbea9db17a

HGVS expressions

NM_004333.6:c.722C>A
NM_004333.6(BRAF):c.722C>A (p.Thr241Lys)
NC_000007.14:g.140801550G>T
CM000669.2:g.140801550G>T
NC_000007.13:g.140501350G>T
CM000669.1:g.140501350G>T
NC_000007.12:g.140147819G>T
NG_007873.3:g.128215C>A
NM_004333.4:c.722C>A
NM_001354609.1:c.722C>A
NM_004333.5:c.722C>A
NR_148928.1:n.1027C>A
NM_001354609.2:c.722C>A
NM_001374244.1:c.722C>A
NM_001374258.1:c.722C>A
ENST00000288602.10:c.722C>A
ENST00000497784.1:n.757C>A

Pathogenic

Met criteria codes 6
PM1 PM2 PS4_Supporting PM6_Strong PP2 PP3

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
RASopathy VCEP
The c.722C>A (p.Thr241Lys) variant in BRAF was absent from large population studies (PM2; gnomad.broadinstitute.org). It has been identified in 1 individual with Noonan syndrome and 1 individual with cardiofaciocutaneous syndrome (PS4_Supporting; Otto von Guericke University Magdeburg internal data, Laboratory for Molecular Medicine internal data; ClinVar SCV000061619.5). It has been reported at least twice as a de novo occurrence without confirmation of maternity or paternity (PM6_Strong; Fulgent Genetics, Laboratory for Molecular Medicine internal data, SCV000061619.5). 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; 29493581). In addition, 3 other pathogenic or likely pathogenic variants have been identified at this codon (PM5 not applied; ClinVar ID: 29805, 29806, 29807). Computational prediction tools and conservation analysis suggest that the p.Thr241Lys variant in BRAF may impact the protein (PP3). This variant is located in BRAF, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic variants are common (PP2; PMID: 29493581). In summary, this variant meets criteria to be classified as pathogenic for autosomal dominant RASopathies. RASopathy-specific ACMG/AMP criteria applied (PMID: 29493581): PS4_Supporting, PM6_Strong, PM1, PM2, PP2, PP3.
Met criteria codes
PM1
Occurs in exon 6 of BRAF, which the EP has defined as a hotspot (PMID: 29493581).
PM2
Absent from both versions of gnomAD.
PS4_Supporting
identified in 1 individual with Noonan syndrome and 1 individual with cardiofaciocutaneous syndrome (PS4_Supporting; Otto von Guericke University Magdeburg internal data, Laboratory for Molecular Medicine internal data; ClinVar SCV000061619.5).
PM6_Strong
Reported at least twice as a de novo variant without confirmation of maternity or paternity (PM6_Strong; Fulgent Genetics, Laboratory for Molecular Medicine internal data, SCV000061619.5).
PP2
BRAF has been specified by the EP to be a missense-constrained gene where pathogenic missense variants are common (PMID: 29493581).
PP3
REVEL 0.946. Entirely conserved in UCSC database. Alamut does not predict an impact to splicing.
Approved on: 2020-06-25
Published on: 2020-07-01
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