1-3069289-A-G
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_022114.4(PRDM16):c.30A>G(p.Leu10=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000442 in 1,538,564 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. L10L) 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 -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRDM16 | NM_022114.4 | c.30A>G | p.Leu10= | synonymous_variant | 1/17 | ENST00000270722.10 | |
LOC124903827 | XM_047436614.1 | c.1651-318T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRDM16 | ENST00000270722.10 | c.30A>G | p.Leu10= | synonymous_variant | 1/17 | 1 | NM_022114.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000673 AC: 1AN: 148490Hom.: 0 Cov.: 29
GnomAD3 exomes AF: 0.0000242 AC: 5AN: 206906Hom.: 0 AF XY: 0.0000262 AC XY: 3AN XY: 114526
GnomAD4 exome AF: 0.0000482 AC: 67AN: 1390074Hom.: 0 Cov.: 30 AF XY: 0.0000492 AC XY: 34AN XY: 690796
GnomAD4 genome ? AF: 0.00000673 AC: 1AN: 148490Hom.: 0 Cov.: 29 AF XY: 0.0000138 AC XY: 1AN XY: 72384
ClinVar
Submissions by phenotype
Left ventricular noncompaction 8 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 10, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at