chr14-104930887-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_138790.5(PLD4):c.863G>A(p.Arg288His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000144 in 1,461,168 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_138790.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLD4 | NM_138790.5 | c.863G>A | p.Arg288His | missense_variant | 7/11 | ENST00000392593.9 | |
PLD4 | NM_001308174.2 | c.884G>A | p.Arg295His | missense_variant | 7/11 | ||
PLD4 | XM_011536411.3 | c.884G>A | p.Arg295His | missense_variant | 7/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLD4 | ENST00000392593.9 | c.863G>A | p.Arg288His | missense_variant | 7/11 | 1 | NM_138790.5 | P2 | |
PLD4 | ENST00000540372.5 | c.884G>A | p.Arg295His | missense_variant | 7/11 | 2 | A2 | ||
PLD4 | ENST00000649344.1 | c.863G>A | p.Arg288His | missense_variant | 7/11 | ||||
PLD4 | ENST00000472702.1 | n.267G>A | non_coding_transcript_exon_variant | 1/3 | 4 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249240Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135318
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461168Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 726864
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 14, 2023 | The c.863G>A (p.R288H) alteration is located in exon 7 (coding exon 6) of the PLD4 gene. This alteration results from a G to A substitution at nucleotide position 863, causing the arginine (R) at amino acid position 288 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at