3-171605321-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_002662.5(PLD1):c.2978G>A(p.Arg993Gln) variant causes a missense change. The variant allele was found at a frequency of 0.00000894 in 1,454,600 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002662.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLD1 | ENST00000351298.9 | c.2978G>A | p.Arg993Gln | missense_variant | Exon 26 of 27 | 1 | NM_002662.5 | ENSP00000342793.4 | ||
PLD1 | ENST00000356327.9 | c.2864G>A | p.Arg955Gln | missense_variant | Exon 25 of 26 | 1 | ENSP00000348681.5 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251258Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135784
GnomAD4 exome AF: 0.00000894 AC: 13AN: 1454600Hom.: 0 Cov.: 29 AF XY: 0.00000691 AC XY: 5AN XY: 724088
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not provided Uncertain:1
In silico analysis indicates that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at