12-2828362-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_031474.3(NRIP2):c.548G>C(p.Arg183Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000111 in 1,614,020 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R183W) has been classified as Uncertain significance.
Frequency
Consequence
NM_031474.3 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 |
---|---|---|---|---|---|---|---|---|
NRIP2 | NM_031474.3 | c.548G>C | p.Arg183Pro | missense_variant | Exon 3 of 6 | ENST00000337508.9 | NP_113662.1 | |
ITFG2 | NR_130744.3 | n.1573-1855C>G | intron_variant | Intron 12 of 13 | ||||
ITFG2 | NR_147202.2 | n.1475-2472C>G | intron_variant | Intron 12 of 15 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152146Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251442Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135892
GnomAD4 exome AF: 0.000120 AC: 175AN: 1461874Hom.: 0 Cov.: 31 AF XY: 0.000114 AC XY: 83AN XY: 727238
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152146Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74310
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.548G>C (p.R183P) alteration is located in exon 3 (coding exon 3) of the NRIP2 gene. This alteration results from a G to C substitution at nucleotide position 548, causing the arginine (R) at amino acid position 183 to be replaced by a proline (P). 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