3-171603294-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_002662.5(PLD1):c.3009G>A(p.Arg1003Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000639 in 1,612,878 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_002662.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLD1 | ENST00000351298.9 | c.3009G>A | p.Arg1003Arg | synonymous_variant | Exon 27 of 27 | 1 | NM_002662.5 | ENSP00000342793.4 | ||
PLD1 | ENST00000356327.9 | c.2895G>A | p.Arg965Arg | synonymous_variant | Exon 26 of 26 | 1 | ENSP00000348681.5 |
Frequencies
GnomAD3 genomes AF: 0.000309 AC: 47AN: 152134Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000919 AC: 23AN: 250342Hom.: 0 AF XY: 0.0000665 AC XY: 9AN XY: 135346
GnomAD4 exome AF: 0.0000383 AC: 56AN: 1460626Hom.: 0 Cov.: 30 AF XY: 0.0000289 AC XY: 21AN XY: 726704
GnomAD4 genome AF: 0.000309 AC: 47AN: 152252Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74438
ClinVar
Submissions by phenotype
PLD1-related disorder Benign:1
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). -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at