chr7-116777421-T-A

Position:

• chr7-116777421-T-A

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 4P and 1B. PM1 PM2 BP4

The ENST00000397752.8(MET):​c.3292T>A​(p.Leu1098Met) 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L1098S) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: MET ENST00000397752.8 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0230

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 3 ACMG points.

• PM1: In a hotspot region, there are 4 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 1 benign, 16 uncertain in ENST00000397752.8
• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.31696653).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MET	NM_000245.4	c.3292T>A	p.Leu1098Met	missense_variant	16/21	ENST00000397752.8	NP_000236.2
MET	NM_001127500.3	c.3346T>A	p.Leu1116Met	missense_variant	16/21		NP_001120972.1
MET	NM_001324402.2	c.2002T>A	p.Leu668Met	missense_variant	15/20		NP_001311331.1
MET	XM_011516223.2	c.3349T>A	p.Leu1117Met	missense_variant	17/22		XP_011514525.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MET	ENST00000397752.8	c.3292T>A	p.Leu1098Met	missense_variant	16/21	1	NM_000245.4	ENSP00000380860	P3
MET	ENST00000318493.11	c.3346T>A	p.Leu1116Met	missense_variant	16/21	1		ENSP00000317272	A2
MET	ENST00000436117.3	c.*897T>A		3_prime_UTR_variant, NMD_transcript_variant	15/20	1		ENSP00000410980

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.098
BayesDel_addAF	Uncertain	0.014	T
BayesDel_noAF	Benign	-0.22
CADD	Benign	20
DANN	Uncertain	0.99
DEOGEN2	Uncertain	0.48	T;.
Eigen	Benign	0.023
Eigen_PC	Benign	-0.012
FATHMM_MKL	Benign	0.71	D
LIST_S2	Benign	0.80	T;T
M_CAP	Uncertain	0.086	D
MetaRNN	Benign	0.32	T;T
MetaSVM	Uncertain	-0.011	T
MutationAssessor	Benign	1.9	L;.
MutationTaster	Benign	1.0	D;D;D
PrimateAI	Uncertain	0.72	T
PROVEAN	Benign	-0.46	N;N
REVEL	Uncertain	0.44
Sift	Uncertain	0.010	D;D
Sift4G	Uncertain	0.039	D;D
Polyphen		1.0	D;D
Vest4		0.37
MutPred		0.35		Gain of methylation at K1103 (P = 0.0531);.;
MVP		0.46
MPC		0.87
ClinPred		0.91	D
GERP RS		1.5
Varity_R		0.56
gMVP		0.52

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr7-116417475;