chr1-74763937-A-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_138467.3(TYW3):c.604A>T(p.Thr202Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000255 in 1,606,406 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_138467.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TYW3 | NM_138467.3 | c.604A>T | p.Thr202Ser | missense_variant | 6/6 | ENST00000370867.8 | |
TYW3 | NM_001162916.2 | c.505A>T | p.Thr169Ser | missense_variant | 5/5 | ||
TYW3 | XM_006710347.3 | c.604A>T | p.Thr202Ser | missense_variant | 6/7 | ||
TYW3 | NR_027962.2 | n.810A>T | non_coding_transcript_exon_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TYW3 | ENST00000370867.8 | c.604A>T | p.Thr202Ser | missense_variant | 6/6 | 1 | NM_138467.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152098Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000736 AC: 18AN: 244546Hom.: 0 AF XY: 0.0000757 AC XY: 10AN XY: 132072
GnomAD4 exome AF: 0.0000241 AC: 35AN: 1454190Hom.: 0 Cov.: 31 AF XY: 0.0000249 AC XY: 18AN XY: 723028
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152216Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74422
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 18, 2023 | The c.604A>T (p.T202S) alteration is located in exon 6 (coding exon 6) of the TYW3 gene. This alteration results from a A to T substitution at nucleotide position 604, causing the threonine (T) at amino acid position 202 to be replaced by a serine (S). 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