rs180177034

chr7-140801536-C-Gchr7-140801536-C-T

Variant summary

Our verdict is Pathogenic. Variant got 17 ACMG points: 17P and 0B. PM1 PM2 PP2 PP3_Strong PP5_Very_Strong

The NM_001374258.1(BRAF):c.736G>C(p.Ala246Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★★). Synonymous variant affecting the same amino acid position (i.e. A246A) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: BRAF NM_001374258.1 missense
• Clinical Significance: Pathogenic reviewed by expert panel P:11
• Conservation: PhyloP100: 7.86

Genes affected

BRAF (HGNC:1097): (B-Raf proto-oncogene, serine/threonine kinase) This gene encodes a protein belonging to the RAF family of serine/threonine protein kinases. This protein plays a role in regulating the MAP kinase/ERK signaling pathway, which affects cell division, differentiation, and secretion. Mutations in this gene, most commonly the V600E mutation, are the most frequently identified cancer-causing mutations in melanoma, and have been identified in various other cancers as well, including non-Hodgkin lymphoma, colorectal cancer, thyroid carcinoma, non-small cell lung carcinoma, hairy cell leukemia and adenocarcinoma of lung. Mutations in this gene are also associated with cardiofaciocutaneous, Noonan, and Costello syndromes, which exhibit overlapping phenotypes. A pseudogene of this gene has been identified on the X chromosome. [provided by RefSeq, Aug 2017]

ACMG classification

Verdict is Pathogenic. Variant got 17 ACMG points.

• PM1: In a hotspot region, there are 5 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 4 uncertain in NM_001374258.1
• PM2: Very rare variant in population databases, with high coverage
• PP2: Missense variant where missense usually causes diseases, BRAF
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.976
• PP5: Variant 7-140801536-C-G is Pathogenic according to our data. Variant chr7-140801536-C-G is described in ClinVar as [Pathogenic]. Clinvar id is 13965.Status of the report is reviewed_by_expert_panel, 3 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRAF	NM_001374258.1	c.736G>C	p.Ala246Pro	missense_variant	6/20	ENST00000644969.2
BRAF	NM_004333.6	c.736G>C	p.Ala246Pro	missense_variant	6/18	ENST00000646891.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRAF	ENST00000644969.2	c.736G>C	p.Ala246Pro	missense_variant	6/20		NM_001374258.1
BRAF	ENST00000646891.2	c.736G>C	p.Ala246Pro	missense_variant	6/18		NM_004333.6	P4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:11

Revision: reviewed by expert panel

Submissions by phenotype

Noonan syndrome 1 Pathogenic:2

Pathogenic, no assertion criteria provided	clinical testing	Molecular Genetics, Centre for Human Genetics	-	- -
Pathogenic, no assertion criteria provided	research	Division of Human Genetics, National Health Laboratory Service/University of the Witwatersrand	-	- -

Cardio-facio-cutaneous syndrome Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Blueprint Genetics	Jan 23, 2015	- -
Pathogenic, reviewed by expert panel	curation	ClinGen RASopathy Variant Curation Expert Panel	Apr 03, 2017	The c.736G>C (p.Ala246Pro) variant in BRAF has been reported in the literature as a de novo occurrence in at least 2 patients with clinical features of a RASopathy (PM6 and PS2; PMID 16474404 and 18042262). In vitro functional studies provide some evidence that the p.Ala246Pro variant may impact protein function (PS3; 16474404, 19376813). This variant was absent from large population studies (PM2; ExAC, http://exac.broadinstitute.org). 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). This variant is in a location which has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot or domain of BRAF (PM1; PMID 29493581). Computational prediction tools and conservation analysis suggest that the p.Ala246Pro variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. Rasopathy-specific ACMG/AMP criteria applied (PMID:29493581): PP2, PP3, PM1, PM2, PM6, PS2, PS3. -

not provided Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Apr 12, 2023	Published functional studies demonstrate a damaging effect that the A246P variant results in increased ELK-dependent transcription, leading to activation of BRAF and stimulation of downstream effectors (MEK and ERK) (Niihori et al., 2006); Not observed in large population cohorts (gnomAD); Missense variants in this gene are often considered pathogenic (HGMD); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 19376813, 24409384, 34573299, 30141192, 20523244, 16474404, 18042262, 23885229, 24803665, 28809097, 28911804, 27666661, 31560489, 35418823, 24957944, 15488754, 16439621, 15520807, 17603483, 29493581, 17704260) -
Pathogenic, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Jun 09, 2020	PP2, PP3, PM1, PM2, PM6, PS2, PS3, PS4 -

Noonan syndrome 7 Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Neuberg Centre For Genomic Medicine, NCGM

-

The missense c.736G>C (p.Ala246Pro) variant in BRAF gene has been reported in heterozygous state in individuals affected with cardio-facio-cutaneous syndrome or Noonan syndrome (Ohtake A et al., 2011). Experimental studies have shown that this missense increased ELK-dependent transcription, leading to activation of BRAF and stimulation of downstream effectors (MEK and ERK) (Niihori et al., 2006). The p.Ala246Pro variant is novel (not in any individuals) in gnomAD and in 1000 genome database. It has been submitted to ClinVar as Pathogenic. The amino acid Ala at position 246 is changed to a Pro changing protein sequence and it might alter its composition and physico-chemical properties. The amino acid change p.Ala246Pro in BRAF is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Pathogenic. -

Noonan syndrome;C1275081:Cardio-facio-cutaneous syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Aug 02, 2013

The p.Ala246Pro variant in BRAF has been reported in 6 individuals with clinical features of Cardio-facio-cutaneous syndrome (CFC) (Niihori 2006, Nava 2007, Nys trom 2008, Schulz 2008, Ohtake 2011). This variant occurred de novo in 2 of thes e individuals (Niihori 2006, Schulz 2008), and one of these individuals also had Non-Hodgkin Lymphoma (Ohtake 2011). Furthermore, this variant has now been iden tified by our laboratory in 5 individuals with clinical features of Noonan syndr ome and/or CFC syndrome. It was also absent from large population studies. There fore, this variant meets our criteria to be classified as pathogenic (http://www .partners.org/personalizedmedicine/LMM). -

Cardiofaciocutaneous syndrome 1 Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Mar 01, 2006

- -

Noonan syndrome Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

Clinical Molecular Genetics Laboratory, Johns Hopkins All Children's Hospital

Jun 15, 2017

- -

RASopathy Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Sep 01, 2022

For these reasons, this variant has been classified as Pathogenic. Experimental studies have shown that this missense change affects BRAF function (PMID: 16474404). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt BRAF protein function. ClinVar contains an entry for this variant (Variation ID: 13965). This missense change has been observed in individuals with cardio-facio-cutaneous syndrome or Noonan syndrome (PMID: 16474404, 20523244, 28911804). This variant is not present in population databases (gnomAD no frequency). This sequence change replaces alanine, which is neutral and non-polar, with proline, which is neutral and non-polar, at codon 246 of the BRAF protein (p.Ala246Pro). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.49	D
BayesDel_noAF	Pathogenic	0.46
Cadd	Pathogenic	33
Dann	Uncertain	1.0
Eigen	Pathogenic	0.92
Eigen_PC	Pathogenic	0.87
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Pathogenic	0.98	D;D;D;D
M_CAP	Pathogenic	0.54	D
MetaRNN	Pathogenic	0.98	D;D;D;D
MetaSVM	Pathogenic	1.0	D
MutationTaster	Benign	1.0	A
PrimateAI	Pathogenic	0.94	D
Polyphen		1.0	.;.;D;.
Vest4		0.94
MutPred		0.90		Loss of catalytic residue at A246 (P = 0.0079);Loss of catalytic residue at A246 (P = 0.0079);Loss of catalytic residue at A246 (P = 0.0079);Loss of catalytic residue at A246 (P = 0.0079);
MVP		0.99
MPC		2.3
ClinPred		0.99	D
GERP RS		5.4
Varity_R		0.95
gMVP		0.99

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs180177034; hg19: chr7-140501336;