rs371015065
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7
The NM_000245.4(MET):c.2769A>C(p.Val923=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000118 in 1,613,806 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. V923V) 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.2769A>C | p.Val923= | synonymous_variant | 13/21 | ENST00000397752.8 | |
MET | NM_001127500.3 | c.2823A>C | p.Val941= | synonymous_variant | 13/21 | ||
MET | NM_001324402.2 | c.1479A>C | p.Val493= | synonymous_variant | 12/20 | ||
MET | XM_011516223.2 | c.2826A>C | p.Val942= | synonymous_variant | 14/22 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MET | ENST00000397752.8 | c.2769A>C | p.Val923= | synonymous_variant | 13/21 | 1 | NM_000245.4 | P3 | |
MET | ENST00000318493.11 | c.2823A>C | p.Val941= | synonymous_variant | 13/21 | 1 | A2 | ||
MET | ENST00000436117.3 | c.*374A>C | 3_prime_UTR_variant, NMD_transcript_variant | 12/20 | 1 | ||||
MET | ENST00000454623.1 | c.165A>C | p.Val55= | synonymous_variant | 2/3 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152234Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249362Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135292
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461572Hom.: 0 Cov.: 32 AF XY: 0.0000124 AC XY: 9AN XY: 727078
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152234Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74378
ClinVar
Submissions by phenotype
Renal cell carcinoma Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 17, 2023 | - - |
Hereditary cancer-predisposing syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 16, 2021 | 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at