2-100284350-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_198461.4(LONRF2):c.2213G>A(p.Arg738His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000754 in 1,590,700 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_198461.4 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 |
---|---|---|---|---|---|---|---|---|
LONRF2 | NM_198461.4 | c.2213G>A | p.Arg738His | missense_variant | Exon 12 of 12 | ENST00000393437.8 | NP_940863.3 | |
LONRF2 | NM_001371783.1 | c.1484G>A | p.Arg495His | missense_variant | Exon 13 of 13 | NP_001358712.1 | ||
LONRF2 | XM_047443537.1 | c.1484G>A | p.Arg495His | missense_variant | Exon 12 of 12 | XP_047299493.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LONRF2 | ENST00000393437.8 | c.2213G>A | p.Arg738His | missense_variant | Exon 12 of 12 | 5 | NM_198461.4 | ENSP00000377086.3 | ||
LONRF2 | ENST00000409647.1 | c.1484G>A | p.Arg495His | missense_variant | Exon 12 of 12 | 2 | ENSP00000386823.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152272Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000470 AC: 1AN: 212732Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 113902
GnomAD4 exome AF: 0.00000765 AC: 11AN: 1438428Hom.: 0 Cov.: 30 AF XY: 0.0000126 AC XY: 9AN XY: 713020
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152272Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74398
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2213G>A (p.R738H) alteration is located in exon 12 (coding exon 12) of the LONRF2 gene. This alteration results from a G to A substitution at nucleotide position 2213, causing the arginine (R) at amino acid position 738 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