chr9-127108539-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_012098.3(ANGPTL2):c.193G>A(p.Val65Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000521 in 1,613,252 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_012098.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANGPTL2 | NM_012098.3 | c.193G>A | p.Val65Ile | missense_variant | 2/5 | ENST00000373425.8 | |
RALGPS1 | NM_014636.3 | c.610+39183C>T | intron_variant | ENST00000259351.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANGPTL2 | ENST00000373425.8 | c.193G>A | p.Val65Ile | missense_variant | 2/5 | 1 | NM_012098.3 | P1 | |
RALGPS1 | ENST00000259351.10 | c.610+39183C>T | intron_variant | 1 | NM_014636.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000462 AC: 7AN: 151386Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000438 AC: 11AN: 251376Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135868
GnomAD4 exome AF: 0.0000527 AC: 77AN: 1461866Hom.: 0 Cov.: 33 AF XY: 0.0000578 AC XY: 42AN XY: 727228
GnomAD4 genome AF: 0.0000462 AC: 7AN: 151386Hom.: 0 Cov.: 31 AF XY: 0.0000541 AC XY: 4AN XY: 73914
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 21, 2021 | The c.193G>A (p.V65I) 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 193, causing the valine (V) at amino acid position 65 to be replaced by an isoleucine (I). 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