rs200815080
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_000353.3(TAT):c.1223C>T(p.Thr408Met) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000199 in 1,611,132 control chromosomes in the GnomAD database, with no homozygous occurrence. 14/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★★). Synonymous variant affecting the same amino acid position (i.e. T408T) has been classified as Likely pathogenic.
Frequency
Consequence
NM_000353.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TAT | NM_000353.3 | c.1223C>T | p.Thr408Met | missense_variant, splice_region_variant | 11/12 | ENST00000355962.5 | |
TAT-AS1 | NR_103852.1 | n.258+2511G>A | intron_variant, non_coding_transcript_variant | ||||
TAT-AS1 | NR_103851.1 | n.284+2511G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TAT | ENST00000355962.5 | c.1223C>T | p.Thr408Met | missense_variant, splice_region_variant | 11/12 | 1 | NM_000353.3 | P1 | |
TAT-AS1 | ENST00000561529.1 | n.284+2511G>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152204Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000800 AC: 2AN: 249990Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135036
GnomAD4 exome AF: 0.0000199 AC: 29AN: 1458928Hom.: 0 Cov.: 30 AF XY: 0.0000207 AC XY: 15AN XY: 725800
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152204Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74358
ClinVar
Submissions by phenotype
Tyrosinemia type II Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 12, 2021 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Counsyl | Apr 12, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at