chr2-218618798-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_032726.4(PLCD4):c.401G>A(p.Arg134His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000315 in 1,587,748 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032726.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLCD4 | NM_032726.4 | c.401G>A | p.Arg134His | missense_variant | 4/16 | ENST00000450993.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLCD4 | ENST00000450993.7 | c.401G>A | p.Arg134His | missense_variant | 4/16 | 1 | NM_032726.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152204Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000444 AC: 9AN: 202878Hom.: 0 AF XY: 0.0000183 AC XY: 2AN XY: 109068
GnomAD4 exome AF: 0.0000293 AC: 42AN: 1435544Hom.: 0 Cov.: 31 AF XY: 0.0000295 AC XY: 21AN XY: 711624
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152204Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74364
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 27, 2022 | The c.401G>A (p.R134H) alteration is located in exon 4 (coding exon 3) of the PLCD4 gene. This alteration results from a G to A substitution at nucleotide position 401, causing the arginine (R) at amino acid position 134 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