chr22-50526673-C-T
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_001953.5(TYMP):c.831G>A(p.Leu277=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00644 in 1,551,898 control chromosomes in the GnomAD database, including 453 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. L277L) has been classified as Likely benign.
Frequency
Consequence
NM_001953.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TYMP | NM_001953.5 | c.831G>A | p.Leu277= | synonymous_variant | 7/10 | ENST00000252029.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TYMP | ENST00000252029.8 | c.831G>A | p.Leu277= | synonymous_variant | 7/10 | 1 | NM_001953.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0320 AC: 4866AN: 152230Hom.: 233 Cov.: 33
GnomAD3 exomes AF: 0.00832 AC: 1221AN: 146814Hom.: 57 AF XY: 0.00647 AC XY: 517AN XY: 79894
GnomAD4 exome AF: 0.00366 AC: 5117AN: 1399550Hom.: 218 Cov.: 36 AF XY: 0.00324 AC XY: 2242AN XY: 691454
GnomAD4 genome ? AF: 0.0320 AC: 4872AN: 152348Hom.: 235 Cov.: 33 AF XY: 0.0314 AC XY: 2336AN XY: 74504
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Apr 30, 2019 | - - |
Benign, no assertion criteria provided | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Feb 29, 2016 | - - |
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 18, 2011 | 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. - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Mitochondrial neurogastrointestinal encephalomyopathy Benign:1
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | Sep 16, 2020 | - - |
Mitochondrial complex IV deficiency, nuclear type 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Mitochondrial DNA depletion syndrome 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Fatal Infantile Cardioencephalomyopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at