9-127108286-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_012098.3(ANGPTL2):c.446G>A(p.Arg149Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,613,866 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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. R149W) has been classified as Uncertain significance.
Frequency
Consequence
NM_012098.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ANGPTL2 | NM_012098.3 | c.446G>A | p.Arg149Gln | missense_variant | Exon 2 of 5 | ENST00000373425.8 | NP_036230.1 | |
RALGPS1 | NM_014636.3 | c.610+38930C>T | intron_variant | Intron 8 of 18 | ENST00000259351.10 | NP_055451.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ANGPTL2 | ENST00000373425.8 | c.446G>A | p.Arg149Gln | missense_variant | Exon 2 of 5 | 1 | NM_012098.3 | ENSP00000362524.3 | ||
RALGPS1 | ENST00000259351.10 | c.610+38930C>T | intron_variant | Intron 8 of 18 | 1 | NM_014636.3 | ENSP00000259351.5 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151988Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251380Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135892
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461878Hom.: 0 Cov.: 33 AF XY: 0.0000124 AC XY: 9AN XY: 727242
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151988Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 74236
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.446G>A (p.R149Q) alteration is located in exon 2 (coding exon 1) of the ANGPTL2 gene. This alteration results from a G to A substitution at nucleotide position 446, causing the arginine (R) at amino acid position 149 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