chr2-233671962-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_021027.3(UGT1A9):c.28C>A(p.Leu10Ile) 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 1,461,354 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
UGT1A9 | NM_021027.3 | c.28C>A | p.Leu10Ile | missense_variant | 1/5 | ENST00000354728.5 | NP_066307.1 | |
UGT1A10 | NM_019075.4 | c.855+34585C>A | intron_variant | ENST00000344644.10 | NP_061948.1 | |||
UGT1A8 | NM_019076.5 | c.855+53400C>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.28C>A | p.Leu10Ile | missense_variant | 1/5 | 1 | NM_021027.3 | ENSP00000346768 | P1 | |
UGT1A10 | ENST00000344644.10 | c.855+34585C>A | intron_variant | 1 | NM_019075.4 | ENSP00000343838 | P1 | |||
UGT1A8 | ENST00000373450.5 | c.855+53400C>A | intron_variant | 1 | NM_019076.5 | ENSP00000362549 | P1 | |||
UGT1A10 | ENST00000373445.1 | c.855+34585C>A | intron_variant | 1 | ENSP00000362544 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000799 AC: 2AN: 250288Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135236
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461354Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 726958
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 26, 2024 | The c.28C>A (p.L10I) alteration is located in exon 1 (coding exon 1) of the UGT1A9 gene. This alteration results from a C to A substitution at nucleotide position 28, causing the leucine (L) at amino acid position 10 to be replaced by an isoleucine (I). 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