rs147601535
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6BP7
The NM_000030.3(AGXT):c.489G>A(p.Leu163Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000208 in 1,599,146 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000030.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AGXT | ENST00000307503.4 | c.489G>A | p.Leu163Leu | synonymous_variant | Exon 4 of 11 | 1 | NM_000030.3 | ENSP00000302620.3 | ||
AGXT | ENST00000472436.1 | n.509G>A | non_coding_transcript_exon_variant | Exon 4 of 5 | 2 | |||||
AGXT | ENST00000476698.1 | n.226G>A | non_coding_transcript_exon_variant | Exon 1 of 4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000177 AC: 27AN: 152192Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000206 AC: 46AN: 223138Hom.: 0 AF XY: 0.000215 AC XY: 26AN XY: 120654
GnomAD4 exome AF: 0.000211 AC: 305AN: 1446954Hom.: 1 Cov.: 31 AF XY: 0.000202 AC XY: 145AN XY: 718344
GnomAD4 genome AF: 0.000177 AC: 27AN: 152192Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 74342
ClinVar
Submissions by phenotype
Primary hyperoxaluria, type I Uncertain:1Benign:1
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not provided Benign:2
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AGXT: BP4, BP7 -
Primary hyperoxaluria Uncertain:1
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not specified Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at