rs200109766
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_022114.4(PRDM16):āc.2187C>Gā(p.Phe729Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000268 in 1,613,456 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_022114.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRDM16 | NM_022114.4 | c.2187C>G | p.Phe729Leu | missense_variant | 9/17 | ENST00000270722.10 | |
PRDM16 | NM_199454.3 | c.2187C>G | p.Phe729Leu | missense_variant | 9/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRDM16 | ENST00000270722.10 | c.2187C>G | p.Phe729Leu | missense_variant | 9/17 | 1 | NM_022114.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000322 AC: 49AN: 152240Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000355 AC: 88AN: 248214Hom.: 0 AF XY: 0.000341 AC XY: 46AN XY: 134838
GnomAD4 exome AF: 0.000263 AC: 384AN: 1461098Hom.: 1 Cov.: 36 AF XY: 0.000308 AC XY: 224AN XY: 726928
GnomAD4 genome ? AF: 0.000322 AC: 49AN: 152358Hom.: 0 Cov.: 33 AF XY: 0.000403 AC XY: 30AN XY: 74502
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Oct 01, 2023 | PRDM16: BP4, BS1 - |
Left ventricular noncompaction 8 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 11, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at