12-2830804-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_031474.3(NRIP2):c.399G>T(p.Gln133His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000123 in 1,461,600 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar 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.399G>T | p.Gln133His | missense_variant | Exon 2 of 6 | ENST00000337508.9 | NP_113662.1 | |
ITFG2 | NR_130744.3 | n.2160C>A | non_coding_transcript_exon_variant | Exon 13 of 14 | ||||
ITFG2 | NR_147202.2 | n.1475-30C>A | intron_variant | Intron 12 of 15 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1461600Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 727106
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.399G>T (p.Q133H) alteration is located in exon 2 (coding exon 2) of the NRIP2 gene. This alteration results from a G to T substitution at nucleotide position 399, causing the glutamine (Q) at amino acid position 133 to be replaced by a histidine (H). 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