4-68565580-A-G
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001077.4(UGT2B17):āc.865T>Cā(p.Leu289Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00066 in 1,369,026 control chromosomes in the GnomAD database, including 220 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_001077.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
UGT2B17 | ENST00000317746.3 | c.865T>C | p.Leu289Leu | synonymous_variant | Exon 3 of 7 | 1 | NM_001077.4 | ENSP00000320401.2 | ||
UGT2B17 | ENST00000684088.1 | c.115T>C | p.Leu39Leu | synonymous_variant | Exon 2 of 5 | ENSP00000507374.1 |
Frequencies
GnomAD3 genomes AF: 0.00102 AC: 128AN: 125488Hom.: 29 Cov.: 20
GnomAD3 exomes AF: 0.000763 AC: 149AN: 195272Hom.: 41 AF XY: 0.000638 AC XY: 67AN XY: 105026
GnomAD4 exome AF: 0.000625 AC: 777AN: 1243470Hom.: 191 Cov.: 30 AF XY: 0.000610 AC XY: 375AN XY: 614356
GnomAD4 genome AF: 0.00100 AC: 126AN: 125556Hom.: 29 Cov.: 20 AF XY: 0.000984 AC XY: 59AN XY: 59930
ClinVar
Submissions by phenotype
UGT2B17-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at