7-116778953-C-G

Position:

• chr7-116778953-C-G

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 6P and 2B. PM1 PM2 PM5 BP4_Moderate

The ENST00000397752.8(MET):​c.3518C>G​(p.Thr1173Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T1173I) has been classified as Pathogenic.

• Frequency: Genomes: not found (cov: 32)
• Consequence: MET ENST00000397752.8 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 2.14

Genes affected

MET (HGNC:7029): (MET proto-oncogene, receptor tyrosine kinase) This gene encodes a member of the receptor tyrosine kinase family of proteins and the product of the proto-oncogene MET. The encoded preproprotein is proteolytically processed to generate alpha and beta subunits that are linked via disulfide bonds to form the mature receptor. Further processing of the beta subunit results in the formation of the M10 peptide, which has been shown to reduce lung fibrosis. Binding of its ligand, hepatocyte growth factor, induces dimerization and activation of the receptor, which plays a role in cellular survival, embryogenesis, and cellular migration and invasion. Mutations in this gene are associated with papillary renal cell carcinoma, hepatocellular carcinoma, and various head and neck cancers. Amplification and overexpression of this gene are also associated with multiple human cancers. [provided by RefSeq, May 2016]

ACMG classification

Verdict is Uncertain_significance. Variant got 4 ACMG points.

• PM1: In a domain Protein kinase (size 267) in uniprot entity MET_HUMAN there are 42 pathogenic changes around while only 14 benign (75%) in ENST00000397752.8
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr7-116778953-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 13888.Status of the report is no_assertion_criteria_provided, 0 stars.
• BP4: Computational evidence support a benign effect (MetaRNN=0.15099481).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MET	NM_000245.4	c.3518C>G	p.Thr1173Ser	missense_variant	17/21	ENST00000397752.8	NP_000236.2
MET	NM_001127500.3	c.3572C>G	p.Thr1191Ser	missense_variant	17/21		NP_001120972.1
MET	NM_001324402.2	c.2228C>G	p.Thr743Ser	missense_variant	16/20		NP_001311331.1
MET	XM_011516223.2	c.3575C>G	p.Thr1192Ser	missense_variant	18/22		XP_011514525.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MET	ENST00000397752.8	c.3518C>G	p.Thr1173Ser	missense_variant	17/21	1	NM_000245.4	ENSP00000380860	P3
MET	ENST00000318493.11	c.3572C>G	p.Thr1191Ser	missense_variant	17/21	1		ENSP00000317272	A2
MET	ENST00000436117.3	c.*1123C>G		3_prime_UTR_variant, NMD_transcript_variant	16/20	1		ENSP00000410980

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Renal cell carcinoma Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Mar 01, 2020

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals with MET-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces threonine with serine at codon 1191 of the MET protein (p.Thr1191Ser). The threonine residue is moderately conserved and there is a small physicochemical difference between threonine and serine. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.073
BayesDel_addAF	Benign	-0.11	T
BayesDel_noAF	Benign	-0.40
CADD	Benign	21
DANN	Benign	0.81
DEOGEN2	Uncertain	0.42	T;.
Eigen	Benign	-0.25
Eigen_PC	Benign	-0.0056
FATHMM_MKL	Uncertain	0.94	D
LIST_S2	Benign	0.56	T;T
M_CAP	Benign	0.029	D
MetaRNN	Benign	0.15	T;T
MetaSVM	Benign	-0.61	T
MutationAssessor	Benign	-0.33	N;.
MutationTaster	Benign	0.54	D;D;D
PrimateAI	Uncertain	0.76	T
PROVEAN	Benign	0.48	N;N
REVEL	Uncertain	0.30
Sift	Benign	0.36	T;T
Sift4G	Benign	0.73	T;T
Polyphen		0.0020	B;B
Vest4		0.31
MutPred		0.34		Gain of disorder (P = 0.0593);.;
MVP		0.47
MPC		1.7
ClinPred		0.33	T
GERP RS		5.5
Varity_R		0.35
gMVP		0.45

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs121913675; hg19: chr7-116419007;