19-14054465-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001145028.2(PALM3):c.1207G>A(p.Glu403Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000286 in 1,399,406 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001145028.2 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 |
---|---|---|---|---|---|---|---|
PALM3 | NM_001145028.2 | c.1207G>A | p.Glu403Lys | missense_variant | 7/7 | ENST00000669674.2 | |
PALM3 | NM_001367327.1 | c.1009G>A | p.Glu337Lys | missense_variant | 5/5 | ||
PALM3 | XM_047438763.1 | c.1126G>A | p.Glu376Lys | missense_variant | 6/6 | ||
PALM3 | XM_047438764.1 | c.1009G>A | p.Glu337Lys | missense_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PALM3 | ENST00000669674.2 | c.1207G>A | p.Glu403Lys | missense_variant | 7/7 | NM_001145028.2 | A2 | ||
PALM3 | ENST00000340790.9 | c.1162G>A | p.Glu388Lys | missense_variant | 6/6 | 5 | P4 | ||
PALM3 | ENST00000661591.1 | c.1087G>A | p.Glu363Lys | missense_variant | 4/4 | A2 | |||
PALM3 | ENST00000589048.2 | c.1009G>A | p.Glu337Lys | missense_variant | 5/5 | 3 | A2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000127 AC: 2AN: 157234Hom.: 0 AF XY: 0.0000120 AC XY: 1AN XY: 83078
GnomAD4 exome AF: 0.00000286 AC: 4AN: 1399406Hom.: 0 Cov.: 32 AF XY: 0.00000435 AC XY: 3AN XY: 690204
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 28, 2023 | The c.1162G>A (p.E388K) alteration is located in exon 6 (coding exon 6) of the PALM3 gene. This alteration results from a G to A substitution at nucleotide position 1162, causing the glutamic acid (E) at amino acid position 388 to be replaced by a lysine (K). 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