rs2286672
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002663.5(PLD2):c.514C>T(p.Arg172Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 1,613,344 control chromosomes in the GnomAD database, including 14,533 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_002663.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLD2 | NM_002663.5 | c.514C>T | p.Arg172Cys | missense_variant | 6/25 | ENST00000263088.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLD2 | ENST00000263088.11 | c.514C>T | p.Arg172Cys | missense_variant | 6/25 | 1 | NM_002663.5 | P1 | |
PLD2 | ENST00000572940.5 | c.514C>T | p.Arg172Cys | missense_variant | 6/25 | 1 | |||
PLD2 | ENST00000575316.1 | c.514C>T | p.Arg172Cys | missense_variant | 6/6 | 4 | |||
PLD2 | ENST00000575246.6 | c.*162C>T | 3_prime_UTR_variant, NMD_transcript_variant | 6/18 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0888 AC: 13506AN: 152082Hom.: 1240 Cov.: 33
GnomAD3 exomes AF: 0.149 AC: 37465AN: 251458Hom.: 4624 AF XY: 0.156 AC XY: 21266AN XY: 135910
GnomAD4 exome AF: 0.103 AC: 150494AN: 1461144Hom.: 13300 Cov.: 35 AF XY: 0.110 AC XY: 79884AN XY: 726926
GnomAD4 genome ? AF: 0.0886 AC: 13491AN: 152200Hom.: 1233 Cov.: 33 AF XY: 0.0995 AC XY: 7402AN XY: 74408
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at