1-167055070-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005814.3(GPA33):c.733G>A(p.Val245Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000291 in 1,613,618 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005814.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GPA33 | NM_005814.3 | c.733G>A | p.Val245Met | missense_variant | Exon 6 of 7 | ENST00000367868.4 | NP_005805.1 | |
GPA33 | XM_017000005.2 | c.409G>A | p.Val137Met | missense_variant | Exon 7 of 8 | XP_016855494.1 | ||
GPA33 | XM_047424480.1 | c.409G>A | p.Val137Met | missense_variant | Exon 8 of 9 | XP_047280436.1 | ||
LOC105371600 | XR_922249.3 | n.82+2304C>T | intron_variant | Intron 1 of 5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GPA33 | ENST00000367868.4 | c.733G>A | p.Val245Met | missense_variant | Exon 6 of 7 | 1 | NM_005814.3 | ENSP00000356842.3 | ||
GPA33 | ENST00000527955.5 | n.824G>A | non_coding_transcript_exon_variant | Exon 6 of 7 | 5 | |||||
ENSG00000227907 | ENST00000417644.1 | n.216+2304C>T | intron_variant | Intron 1 of 1 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152208Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251002Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135674
GnomAD4 exome AF: 0.0000294 AC: 43AN: 1461410Hom.: 0 Cov.: 32 AF XY: 0.0000261 AC XY: 19AN XY: 727064
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152208Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74364
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.733G>A (p.V245M) alteration is located in exon 6 (coding exon 6) of the GPA33 gene. This alteration results from a G to A substitution at nucleotide position 733, causing the valine (V) at amino acid position 245 to be replaced by a methionine (M). 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