chr19-40366788-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_ModerateBP6_ModerateBP7
The NM_012268.4(PLD3):c.118C>T(p.Leu40=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000547 in 1,461,680 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 (★).
Frequency
Consequence
NM_012268.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLD3 | NM_012268.4 | c.118C>T | p.Leu40= | synonymous_variant | 5/13 | ENST00000409735.9 | |
PLD3 | NM_001031696.4 | c.118C>T | p.Leu40= | synonymous_variant | 5/13 | ||
PLD3 | NM_001291311.2 | c.118C>T | p.Leu40= | synonymous_variant | 5/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLD3 | ENST00000409735.9 | c.118C>T | p.Leu40= | synonymous_variant | 5/13 | 1 | NM_012268.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461680Hom.: 0 Cov.: 32 AF XY: 0.00000413 AC XY: 3AN XY: 727134
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 30, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.