3-49024514-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM1PM2PP3
The NM_000884.3(IMPDH2):c.1504G>A(p.Gly502Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,892 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000884.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IMPDH2 | NM_000884.3 | c.1504G>A | p.Gly502Ser | missense_variant | Exon 13 of 14 | ENST00000326739.9 | NP_000875.2 | |
IMPDH2 | NM_001410759.1 | c.1576G>A | p.Gly526Ser | missense_variant | Exon 14 of 15 | NP_001397688.1 | ||
IMPDH2 | NM_001410760.1 | c.1501G>A | p.Gly501Ser | missense_variant | Exon 13 of 14 | NP_001397689.1 | ||
IMPDH2 | NM_001410761.1 | c.1429G>A | p.Gly477Ser | missense_variant | Exon 12 of 13 | NP_001397690.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IMPDH2 | ENST00000326739.9 | c.1504G>A | p.Gly502Ser | missense_variant | Exon 13 of 14 | 1 | NM_000884.3 | ENSP00000321584.4 | ||
ENSG00000290315 | ENST00000703936.1 | c.3544G>A | p.Gly1182Ser | missense_variant | Exon 21 of 22 | ENSP00000515567.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461892Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 727248
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1504G>A (p.G502S) alteration is located in exon 13 (coding exon 13) of the IMPDH2 gene. This alteration results from a G to A substitution at nucleotide position 1504, causing the glycine (G) at amino acid position 502 to be replaced by a serine (S). 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
Publications
No publications associated with this variant yet.