10-46549478-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001385282.1(GPRIN2):c.1259G>A(p.Arg420Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000161 in 1,611,442 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 8/12 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001385282.1 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPRIN2 | NM_001385282.1 | c.1259G>A | p.Arg420Gln | missense_variant | 3/3 | ENST00000374314.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPRIN2 | ENST00000374314.6 | c.1259G>A | p.Arg420Gln | missense_variant | 3/3 | NM_001385282.1 | P1 | ||
GPRIN2 | ENST00000374317.2 | c.1259G>A | p.Arg420Gln | missense_variant | 3/3 | 3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152308Hom.: 0 Cov.: 78
GnomAD3 exomes AF: 0.0000205 AC: 5AN: 244448Hom.: 0 AF XY: 0.0000150 AC XY: 2AN XY: 132976
GnomAD4 exome AF: 0.0000164 AC: 24AN: 1459016Hom.: 0 Cov.: 119 AF XY: 0.0000138 AC XY: 10AN XY: 725510
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152426Hom.: 0 Cov.: 78 AF XY: 0.00 AC XY: 0AN XY: 74546
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 06, 2021 | The c.1259G>A (p.R420Q) 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 1259, causing the arginine (R) at amino acid position 420 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