7-116757661-G-A
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7
The NM_000245.4(MET):c.1989G>A(p.Ser663=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000297 in 1,613,660 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. S663S) has been classified as Likely benign.
Frequency
Consequence
NM_000245.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MET | NM_000245.4 | c.1989G>A | p.Ser663= | synonymous_variant | 8/21 | ENST00000397752.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MET | ENST00000397752.8 | c.1989G>A | p.Ser663= | synonymous_variant | 8/21 | 1 | NM_000245.4 | P3 | |
MET | ENST00000318493.11 | c.1989G>A | p.Ser663= | synonymous_variant | 8/21 | 1 | A2 | ||
MET | ENST00000436117.3 | c.1989G>A | p.Ser663= | synonymous_variant, NMD_transcript_variant | 8/20 | 1 | |||
MET | ENST00000422097.2 | c.1989G>A | p.Ser663= | synonymous_variant | 8/12 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000658 AC: 10AN: 151956Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000401 AC: 10AN: 249326Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135276
GnomAD4 exome AF: 0.0000260 AC: 38AN: 1461704Hom.: 0 Cov.: 32 AF XY: 0.0000275 AC XY: 20AN XY: 727140
GnomAD4 genome AF: 0.0000658 AC: 10AN: 151956Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74204
ClinVar
Submissions by phenotype
Hereditary cancer-predisposing syndrome Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 13, 2016 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Likely benign, criteria provided, single submitter | curation | Sema4, Sema4 | Jan 25, 2022 | - - |
Renal cell carcinoma Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 28, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2022 | MET: BP4, BP7 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at