10-46549424-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001385282.1(GPRIN2):c.1313G>A(p.Arg438Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000662 in 1,572,162 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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. R438W) has been classified as Uncertain significance.
Frequency
Consequence
NM_001385282.1 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 |
---|---|---|---|---|---|---|---|---|
GPRIN2 | NM_001385282.1 | c.1313G>A | p.Arg438Gln | missense_variant | Exon 3 of 3 | ENST00000374314.6 | NP_001372211.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GPRIN2 | ENST00000374314.6 | c.1313G>A | p.Arg438Gln | missense_variant | Exon 3 of 3 | 6 | NM_001385282.1 | ENSP00000363433.4 | ||
GPRIN2 | ENST00000374317.2 | c.1313G>A | p.Arg438Gln | missense_variant | Exon 3 of 3 | 3 | ENSP00000363436.1 |
Frequencies
GnomAD3 genomes AF: 0.0000919 AC: 14AN: 152292Hom.: 0 Cov.: 78
GnomAD3 exomes AF: 0.0000316 AC: 6AN: 189750Hom.: 0 AF XY: 0.0000391 AC XY: 4AN XY: 102276
GnomAD4 exome AF: 0.0000634 AC: 90AN: 1419870Hom.: 0 Cov.: 101 AF XY: 0.0000598 AC XY: 42AN XY: 702370
GnomAD4 genome AF: 0.0000919 AC: 14AN: 152292Hom.: 0 Cov.: 78 AF XY: 0.0000403 AC XY: 3AN XY: 74410
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1313G>A (p.R438Q) alteration is located in exon 3 (coding exon 1) of the GPRIN2 gene. This alteration results from a G to A substitution at nucleotide position 1313, causing the arginine (R) at amino acid position 438 to be replaced by a glutamine (Q). 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