2-233672032-T-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_021027.3(UGT1A9):c.98T>C(p.Met33Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0115 in 1,614,136 control chromosomes in the GnomAD database, including 132 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_021027.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UGT1A9 | NM_021027.3 | c.98T>C | p.Met33Thr | missense_variant | 1/5 | ENST00000354728.5 | |
UGT1A10 | NM_019075.4 | c.855+34655T>C | intron_variant | ENST00000344644.10 | |||
UGT1A8 | NM_019076.5 | c.855+53470T>C | intron_variant | ENST00000373450.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UGT1A9 | ENST00000354728.5 | c.98T>C | p.Met33Thr | missense_variant | 1/5 | 1 | NM_021027.3 | P1 | |
UGT1A10 | ENST00000344644.10 | c.855+34655T>C | intron_variant | 1 | NM_019075.4 | P1 | |||
UGT1A8 | ENST00000373450.5 | c.855+53470T>C | intron_variant | 1 | NM_019076.5 | P1 | |||
UGT1A10 | ENST00000373445.1 | c.855+34655T>C | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00907 AC: 1381AN: 152188Hom.: 11 Cov.: 32
GnomAD3 exomes AF: 0.00972 AC: 2443AN: 251228Hom.: 16 AF XY: 0.0101 AC XY: 1374AN XY: 135750
GnomAD4 exome AF: 0.0117 AC: 17139AN: 1461830Hom.: 121 Cov.: 33 AF XY: 0.0117 AC XY: 8481AN XY: 727202
GnomAD4 genome ? AF: 0.00905 AC: 1379AN: 152306Hom.: 11 Cov.: 32 AF XY: 0.00826 AC XY: 615AN XY: 74466
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2023 | UGT1A9: BP4, BS1, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at