chr3-171603233-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_002662.5(PLD1):c.3070G>A(p.Val1024Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00294 in 1,613,990 control chromosomes in the GnomAD database, including 28 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_002662.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLD1 | NM_002662.5 | c.3070G>A | p.Val1024Ile | missense_variant | 27/27 | ENST00000351298.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLD1 | ENST00000351298.9 | c.3070G>A | p.Val1024Ile | missense_variant | 27/27 | 1 | NM_002662.5 | A1 | |
PLD1 | ENST00000356327.9 | c.2956G>A | p.Val986Ile | missense_variant | 26/26 | 1 | P4 |
Frequencies
GnomAD3 genomes AF: 0.00681 AC: 1036AN: 152146Hom.: 10 Cov.: 32
GnomAD3 exomes AF: 0.00242 AC: 607AN: 251102Hom.: 3 AF XY: 0.00216 AC XY: 293AN XY: 135706
GnomAD4 exome AF: 0.00253 AC: 3705AN: 1461726Hom.: 18 Cov.: 31 AF XY: 0.00240 AC XY: 1742AN XY: 727168
GnomAD4 genome AF: 0.00685 AC: 1043AN: 152264Hom.: 10 Cov.: 32 AF XY: 0.00674 AC XY: 502AN XY: 74448
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 13, 2024 | - - |
PLD1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 10, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at