chr12-98515918-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_ModerateBP6_Very_StrongBS2
The NM_001032283.3(TMPO):c.51G>A(p.Lys17Lys) variant causes a synonymous change. The variant allele was found at a frequency of 0.0000316 in 1,613,652 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 (★★).
Frequency
Consequence
NM_001032283.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TMPO | NM_001032283.3 | c.51G>A | p.Lys17Lys | synonymous_variant | Exon 1 of 9 | ENST00000556029.6 | NP_001027454.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152194Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000440 AC: 11AN: 249738Hom.: 0 AF XY: 0.0000517 AC XY: 7AN XY: 135424
GnomAD4 exome AF: 0.0000315 AC: 46AN: 1461458Hom.: 0 Cov.: 31 AF XY: 0.0000289 AC XY: 21AN XY: 727060
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152194Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74344
ClinVar
Submissions by phenotype
not specified Benign:1
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. -
Loeys-Dietz syndrome 2 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at