rs17868323
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_019077.3(UGT1A7):c.387T>A(p.Asn129Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000661 in 151,238 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Benignin ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N129R) has been classified as Likely benign.
Frequency
Consequence
NM_019077.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UGT1A7 | NM_019077.3 | c.387T>A | p.Asn129Lys | missense_variant | 1/5 | ENST00000373426.4 | |
UGT1A10 | NM_019075.4 | c.855+44947T>A | intron_variant | ENST00000344644.10 | |||
UGT1A8 | NM_019076.5 | c.855+63762T>A | intron_variant | ENST00000373450.5 | |||
UGT1A9 | NM_021027.3 | c.855+9535T>A | intron_variant | ENST00000354728.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UGT1A7 | ENST00000373426.4 | c.387T>A | p.Asn129Lys | missense_variant | 1/5 | 1 | NM_019077.3 | P1 | |
UGT1A10 | ENST00000344644.10 | c.855+44947T>A | intron_variant | 1 | NM_019075.4 | P1 | |||
UGT1A9 | ENST00000354728.5 | c.855+9535T>A | intron_variant | 1 | NM_021027.3 | P1 | |||
UGT1A8 | ENST00000373450.5 | c.855+63762T>A | intron_variant | 1 | NM_019076.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000661 AC: 1AN: 151238Hom.: 0 Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000274 AC: 4AN: 1461652Hom.: 0 Cov.: 101 AF XY: 0.00000413 AC XY: 3AN XY: 727098
GnomAD4 genome AF: 0.00000661 AC: 1AN: 151238Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 73792
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at