chr2-233672487-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_021027.3(UGT1A9):c.553G>A(p.Ala185Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,646 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
UGT1A9 | NM_021027.3 | c.553G>A | p.Ala185Thr | missense_variant | 1/5 | ENST00000354728.5 | NP_066307.1 | |
UGT1A10 | NM_019075.4 | c.855+35110G>A | intron_variant | ENST00000344644.10 | NP_061948.1 | |||
UGT1A8 | NM_019076.5 | c.855+53925G>A | intron_variant | ENST00000373450.5 | NP_061949.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
UGT1A9 | ENST00000354728.5 | c.553G>A | p.Ala185Thr | missense_variant | 1/5 | 1 | NM_021027.3 | ENSP00000346768 | P1 | |
UGT1A10 | ENST00000344644.10 | c.855+35110G>A | intron_variant | 1 | NM_019075.4 | ENSP00000343838 | P1 | |||
UGT1A8 | ENST00000373450.5 | c.855+53925G>A | intron_variant | 1 | NM_019076.5 | ENSP00000362549 | P1 | |||
UGT1A10 | ENST00000373445.1 | c.855+35110G>A | intron_variant | 1 | ENSP00000362544 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 250968Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135620
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461646Hom.: 0 Cov.: 33 AF XY: 0.00000275 AC XY: 2AN XY: 727132
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 30, 2024 | The c.553G>A (p.A185T) alteration is located in exon 1 (coding exon 1) of the UGT1A9 gene. This alteration results from a G to A substitution at nucleotide position 553, causing the alanine (A) at amino acid position 185 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