rs572092688
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_022114.4(PRDM16):c.2798G>A(p.Arg933Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000885 in 1,468,138 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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. R933W) has been classified as Likely benign.
Frequency
Consequence
NM_022114.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRDM16 | NM_022114.4 | c.2798G>A | p.Arg933Gln | missense_variant | 11/17 | ENST00000270722.10 | |
PRDM16 | NM_199454.3 | c.2798G>A | p.Arg933Gln | missense_variant | 11/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRDM16 | ENST00000270722.10 | c.2798G>A | p.Arg933Gln | missense_variant | 11/17 | 1 | NM_022114.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000139 AC: 2AN: 143866Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000124 AC: 3AN: 242070Hom.: 0 AF XY: 0.00000759 AC XY: 1AN XY: 131788
GnomAD4 exome AF: 0.00000831 AC: 11AN: 1324178Hom.: 0 Cov.: 35 AF XY: 0.00000455 AC XY: 3AN XY: 659142
GnomAD4 genome ? AF: 0.0000139 AC: 2AN: 143960Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 70036
ClinVar
Submissions by phenotype
Left ventricular noncompaction 8 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Oct 18, 2022 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C35"). ClinVar contains an entry for this variant (Variation ID: 576146). This variant has not been reported in the literature in individuals affected with PRDM16-related conditions. This variant is present in population databases (rs572092688, gnomAD 0.01%). This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 933 of the PRDM16 protein (p.Arg933Gln). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at