2-233672698-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_021027.3(UGT1A9):c.764C>T(p.Thr255Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000378 in 1,613,786 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_021027.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UGT1A9 | NM_021027.3 | c.764C>T | p.Thr255Met | missense_variant | 1/5 | ENST00000354728.5 | |
UGT1A10 | NM_019075.4 | c.855+35321C>T | intron_variant | ENST00000344644.10 | |||
UGT1A8 | NM_019076.5 | c.855+54136C>T | intron_variant | ENST00000373450.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UGT1A9 | ENST00000354728.5 | c.764C>T | p.Thr255Met | missense_variant | 1/5 | 1 | NM_021027.3 | P1 | |
UGT1A10 | ENST00000344644.10 | c.855+35321C>T | intron_variant | 1 | NM_019075.4 | P1 | |||
UGT1A8 | ENST00000373450.5 | c.855+54136C>T | intron_variant | 1 | NM_019076.5 | P1 | |||
UGT1A10 | ENST00000373445.1 | c.855+35321C>T | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152150Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000399 AC: 10AN: 250918Hom.: 0 AF XY: 0.0000443 AC XY: 6AN XY: 135584
GnomAD4 exome AF: 0.0000383 AC: 56AN: 1461636Hom.: 0 Cov.: 33 AF XY: 0.0000385 AC XY: 28AN XY: 727134
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152150Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74330
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 26, 2023 | The c.764C>T (p.T255M) alteration is located in exon 1 (coding exon 1) of the UGT1A9 gene. This alteration results from a C to T substitution at nucleotide position 764, causing the threonine (T) at amino acid position 255 to be replaced by a methionine (M). 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