chr18-657785-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_001071.4(TYMS):c.43C>T(p.Pro15Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00539 in 1,452,330 control chromosomes in the GnomAD database, including 41 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001071.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TYMS | NM_001071.4 | c.43C>T | p.Pro15Ser | missense_variant | 1/7 | ENST00000323274.15 | |
TYMSOS | NR_171001.1 | n.450+57G>A | intron_variant, non_coding_transcript_variant | ||||
TYMS | NM_001354867.2 | c.43C>T | p.Pro15Ser | missense_variant | 1/6 | ||
TYMS | NM_001354868.2 | c.43C>T | p.Pro15Ser | missense_variant | 1/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TYMS | ENST00000323274.15 | c.43C>T | p.Pro15Ser | missense_variant | 1/7 | 1 | NM_001071.4 | P1 | |
TYMSOS | ENST00000585033.1 | n.428+57G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00386 AC: 587AN: 151964Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00424 AC: 217AN: 51128Hom.: 0 AF XY: 0.00453 AC XY: 135AN XY: 29806
GnomAD4 exome AF: 0.00557 AC: 7243AN: 1300256Hom.: 41 Cov.: 31 AF XY: 0.00549 AC XY: 3506AN XY: 638576
GnomAD4 genome ? AF: 0.00386 AC: 587AN: 152074Hom.: 0 Cov.: 32 AF XY: 0.00374 AC XY: 278AN XY: 74350
ClinVar
Submissions by phenotype
TYMS-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 21, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at