7-116699058-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_000245.4(MET):c.-14-13C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00167 in 1,613,674 control chromosomes in the GnomAD database, including 37 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_000245.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MET | NM_000245.4 | c.-14-13C>T | intron_variant | Intron 1 of 20 | ENST00000397752.8 | NP_000236.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00924 AC: 1406AN: 152118Hom.: 18 Cov.: 32
GnomAD3 exomes AF: 0.00221 AC: 552AN: 249266Hom.: 9 AF XY: 0.00169 AC XY: 228AN XY: 135258
GnomAD4 exome AF: 0.000875 AC: 1279AN: 1461438Hom.: 18 Cov.: 31 AF XY: 0.000750 AC XY: 545AN XY: 727020
GnomAD4 genome AF: 0.00932 AC: 1419AN: 152236Hom.: 19 Cov.: 32 AF XY: 0.00841 AC XY: 626AN XY: 74452
ClinVar
Submissions by phenotype
not provided Benign:2
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not specified Benign:1
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Papillary renal cell carcinoma type 1 Benign: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 and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at