chr2-218634129-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_032726.4(PLCD4):c.1631C>T(p.Thr544Ile) variant causes a missense change. The variant allele was found at a frequency of 0.00000137 in 1,459,704 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLCD4 | ENST00000450993.7 | c.1631C>T | p.Thr544Ile | missense_variant | Exon 12 of 16 | 1 | NM_032726.4 | ENSP00000388631.2 | ||
PLCD4 | ENST00000432688.5 | c.1727C>T | p.Thr576Ile | missense_variant | Exon 13 of 17 | 5 | ENSP00000396185.1 | |||
PLCD4 | ENST00000417849.5 | c.1631C>T | p.Thr544Ile | missense_variant | Exon 12 of 17 | 5 | ENSP00000396942.1 | |||
ZNF142 | ENST00000411696 | c.*4210G>A | 3_prime_UTR_variant | Exon 11 of 11 | 5 | NM_001379659.1 | ENSP00000398798.3 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000407 AC: 1AN: 245494Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 133080
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1459704Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 725890
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1631C>T (p.T544I) alteration is located in exon 12 (coding exon 11) of the PLCD4 gene. This alteration results from a C to T substitution at nucleotide position 1631, causing the threonine (T) at amino acid position 544 to be replaced by an isoleucine (I). 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