chr2-218634514-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_032726.4(PLCD4):c.1780C>T(p.Arg594Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000366 in 1,613,894 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLCD4 | ENST00000450993.7 | c.1780C>T | p.Arg594Cys | missense_variant | Exon 13 of 16 | 1 | NM_032726.4 | ENSP00000388631.2 | ||
PLCD4 | ENST00000432688.5 | c.1876C>T | p.Arg626Cys | missense_variant | Exon 14 of 17 | 5 | ENSP00000396185.1 | |||
PLCD4 | ENST00000417849.5 | c.1780C>T | p.Arg594Cys | missense_variant | Exon 13 of 17 | 5 | ENSP00000396942.1 | |||
ZNF142 | ENST00000411696 | c.*3825G>A | 3_prime_UTR_variant | Exon 11 of 11 | 5 | NM_001379659.1 | ENSP00000398798.3 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152186Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000321 AC: 8AN: 249264Hom.: 0 AF XY: 0.0000370 AC XY: 5AN XY: 135228
GnomAD4 exome AF: 0.0000349 AC: 51AN: 1461708Hom.: 0 Cov.: 31 AF XY: 0.0000371 AC XY: 27AN XY: 727136
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152186Hom.: 0 Cov.: 33 AF XY: 0.0000673 AC XY: 5AN XY: 74332
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1780C>T (p.R594C) alteration is located in exon 13 (coding exon 12) of the PLCD4 gene. This alteration results from a C to T substitution at nucleotide position 1780, causing the arginine (R) at amino acid position 594 to be replaced by a cysteine (C). 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