rs3807997

chr7-116780504-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000245.4(MET):c.3523-1484C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 152,038 control chromosomes in the GnomAD database, including 2,345 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.17 (2345 hom., cov: 32)
• Consequence: MET NM_000245.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.490

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MET	NM_000245.4	c.3523-1484C>A		intron_variant		ENST00000397752.8
MET	NM_001127500.3	c.3577-1484C>A		intron_variant
MET	NM_001324402.2	c.2233-1484C>A		intron_variant
MET	XM_011516223.2	c.3580-1484C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MET	ENST00000397752.8	c.3523-1484C>A		intron_variant		1	NM_000245.4	P3
MET	ENST00000318493.11	c.3577-1484C>A		intron_variant		1		A2
MET	ENST00000436117.3	c.*1128-1484C>A		intron_variant, NMD_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.171 AC: 26016 AN: 151920 Hom.: 2345 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.160

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.171 AC: 26022 AN: 152038 Hom.: 2345 Cov.: 32 AF XY: 0.172 AC XY: 12764 AN XY: 74304

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.125

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.283

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.193

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.161

Alfa AF: 0.177 Hom.: 454

Bravo AF: 0.162

Asia WGS AF: 0.253 AC: 879 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.9
Dann	Benign	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

LitVar

Other links and lift over

dbSNP: rs3807997; hg19: chr7-116420558;