7-116741050-A-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000245.4(MET):c.1701+25A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00533 in 1,606,758 control chromosomes in the GnomAD database, including 383 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.1701+25A>G | intron_variant | Intron 5 of 20 | ENST00000397752.8 | NP_000236.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0287 AC: 4300AN: 150084Hom.: 210 Cov.: 32
GnomAD3 exomes AF: 0.00728 AC: 1774AN: 243726Hom.: 88 AF XY: 0.00534 AC XY: 705AN XY: 131916
GnomAD4 exome AF: 0.00293 AC: 4261AN: 1456632Hom.: 172 Cov.: 33 AF XY: 0.00252 AC XY: 1822AN XY: 724332
GnomAD4 genome AF: 0.0287 AC: 4307AN: 150126Hom.: 211 Cov.: 32 AF XY: 0.0279 AC XY: 2045AN XY: 73168
ClinVar
Submissions by phenotype
not provided Benign:2
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This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
not specified Benign:1Other:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at