chr2-199948471-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001039693.3(TYW5):āc.80G>Cā(p.Arg27Thr) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.0000719 in 1,613,766 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001039693.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TYW5 | NM_001039693.3 | c.80G>C | p.Arg27Thr | missense_variant, splice_region_variant | 2/8 | ENST00000354611.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TYW5 | ENST00000354611.9 | c.80G>C | p.Arg27Thr | missense_variant, splice_region_variant | 2/8 | 1 | NM_001039693.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152124Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000802 AC: 2AN: 249228Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135212
GnomAD4 exome AF: 0.0000739 AC: 108AN: 1461642Hom.: 0 Cov.: 31 AF XY: 0.0000605 AC XY: 44AN XY: 727098
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152124Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74318
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 12, 2023 | The c.80G>C (p.R27T) alteration is located in exon 2 (coding exon 2) of the TYW5 gene. This alteration results from a G to C substitution at nucleotide position 80, causing the arginine (R) at amino acid position 27 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at