7-116695774-G-C
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBS1_SupportingBS2
The ENST00000456159.1(MET):āc.18G>Cā(p.Lys6Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00126 in 491,904 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/13 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).
Frequency
Consequence
ENST00000456159.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MET | NM_000245.4 | c.-14-3297G>C | intron_variant | Intron 1 of 20 | ENST00000397752.8 | NP_000236.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00331 AC: 504AN: 152174Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.000542 AC: 80AN: 147618Hom.: 0 AF XY: 0.000540 AC XY: 43AN XY: 79566
GnomAD4 exome AF: 0.000333 AC: 113AN: 339612Hom.: 0 Cov.: 0 AF XY: 0.000280 AC XY: 53AN XY: 189500
GnomAD4 genome AF: 0.00332 AC: 505AN: 152292Hom.: 2 Cov.: 32 AF XY: 0.00322 AC XY: 240AN XY: 74474
ClinVar
Submissions by phenotype
not specified Other:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at