1-167063714-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_005814.3(GPA33):c.439G>A(p.Gly147Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000992 in 1,613,104 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G147V) has been classified as Uncertain significance.
Frequency
Consequence
NM_005814.3 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GPA33 | NM_005814.3 | c.439G>A | p.Gly147Ser | missense_variant | Exon 4 of 7 | ENST00000367868.4 | NP_005805.1 | |
GPA33 | XM_017000005.2 | c.115G>A | p.Gly39Ser | missense_variant | Exon 5 of 8 | XP_016855494.1 | ||
GPA33 | XM_047424480.1 | c.115G>A | p.Gly39Ser | missense_variant | Exon 6 of 9 | XP_047280436.1 | ||
LOC105371600 | XR_922249.3 | n.545+597C>T | intron_variant | Intron 5 of 5 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152044Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251314Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135834
GnomAD4 exome AF: 0.00000890 AC: 13AN: 1461060Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 726828
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152044Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74272
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.439G>A (p.G147S) alteration is located in exon 4 (coding exon 4) of the GPA33 gene. This alteration results from a G to A substitution at nucleotide position 439, causing the glycine (G) at amino acid position 147 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