rs201769516
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_022114.4(PRDM16):c.1797G>A(p.Ser599=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000209 in 1,613,610 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 Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. S599S) has been classified as Likely benign.
Frequency
Consequence
NM_022114.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRDM16 | NM_022114.4 | c.1797G>A | p.Ser599= | synonymous_variant | 9/17 | ENST00000270722.10 | |
PRDM16 | NM_199454.3 | c.1797G>A | p.Ser599= | synonymous_variant | 9/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRDM16 | ENST00000270722.10 | c.1797G>A | p.Ser599= | synonymous_variant | 9/17 | 1 | NM_022114.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000230 AC: 35AN: 152144Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000325 AC: 81AN: 249074Hom.: 0 AF XY: 0.000348 AC XY: 47AN XY: 135242
GnomAD4 exome AF: 0.000207 AC: 302AN: 1461348Hom.: 0 Cov.: 37 AF XY: 0.000259 AC XY: 188AN XY: 726988
GnomAD4 genome ? AF: 0.000236 AC: 36AN: 152262Hom.: 0 Cov.: 33 AF XY: 0.000201 AC XY: 15AN XY: 74442
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Aug 19, 2023 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 28, 2021 | - - |
PRDM16-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 15, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Left ventricular noncompaction 8 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 19, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at