rs371654192
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM5BP4_StrongBP6_Very_StrongBS2
The NM_022114.4(PRDM16):c.2468G>A(p.Arg823His) variant causes a missense change. The variant allele was found at a frequency of 0.000251 in 1,524,294 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R823C) has been classified as Uncertain significance.
Frequency
Consequence
NM_022114.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRDM16 | NM_022114.4 | c.2468G>A | p.Arg823His | missense_variant | 9/17 | ENST00000270722.10 | |
PRDM16 | NM_199454.3 | c.2468G>A | p.Arg823His | missense_variant | 9/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRDM16 | ENST00000270722.10 | c.2468G>A | p.Arg823His | missense_variant | 9/17 | 1 | NM_022114.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000401 AC: 61AN: 152208Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000471 AC: 63AN: 133652Hom.: 0 AF XY: 0.000572 AC XY: 42AN XY: 73440
GnomAD4 exome AF: 0.000234 AC: 321AN: 1371968Hom.: 2 Cov.: 36 AF XY: 0.000274 AC XY: 185AN XY: 674654
GnomAD4 genome AF: 0.000400 AC: 61AN: 152326Hom.: 0 Cov.: 33 AF XY: 0.000591 AC XY: 44AN XY: 74484
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 19, 2017 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Left ventricular noncompaction 8 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 27, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at