2-218636273-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.2063G>A(p.Cys688Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000105 in 1,613,916 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 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.2063G>A | p.Cys688Tyr | missense_variant | 15/16 | ENST00000450993.7 | |
ZNF142 | NM_001379659.1 | c.*2066C>T | 3_prime_UTR_variant | 11/11 | ENST00000411696.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLCD4 | ENST00000450993.7 | c.2063G>A | p.Cys688Tyr | missense_variant | 15/16 | 1 | NM_032726.4 | P1 | |
ZNF142 | ENST00000411696.7 | c.*2066C>T | 3_prime_UTR_variant | 11/11 | 5 | NM_001379659.1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152206Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000201 AC: 5AN: 249288Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135242
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461710Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 10AN XY: 727138
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152206Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 05, 2024 | The c.2063G>A (p.C688Y) alteration is located in exon 15 (coding exon 14) of the PLCD4 gene. This alteration results from a G to A substitution at nucleotide position 2063, causing the cysteine (C) at amino acid position 688 to be replaced by a tyrosine (Y). 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