7-116672435-T-G
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 0P and 3B. BP4_ModerateBS1_Supporting
The NM_000245.4(MET):c.-157T>G variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000355 in 394,470 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 Uncertain significance (★).
Frequency
Consequence
NM_000245.4 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MET | NM_000245.4 | c.-157T>G | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 21 | ENST00000397752.8 | NP_000236.2 | ||
MET | NM_000245.4 | c.-157T>G | 5_prime_UTR_variant | Exon 1 of 21 | ENST00000397752.8 | NP_000236.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MET | ENST00000397752 | c.-157T>G | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 21 | 1 | NM_000245.4 | ENSP00000380860.3 | |||
MET | ENST00000397752 | c.-157T>G | 5_prime_UTR_variant | Exon 1 of 21 | 1 | NM_000245.4 | ENSP00000380860.3 |
Frequencies
GnomAD3 genomes AF: 0.00000659 AC: 1AN: 151680Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000535 AC: 13AN: 242790Hom.: 0 Cov.: 0 AF XY: 0.0000568 AC XY: 7AN XY: 123258
GnomAD4 genome AF: 0.00000659 AC: 1AN: 151680Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74072
ClinVar
Submissions by phenotype
Papillary renal cell carcinoma type 1 Uncertain:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at