19-14054476-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001145028.2(PALM3):c.1196C>T(p.Thr399Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000135 in 1,550,984 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PALM3 | NM_001145028.2 | c.1196C>T | p.Thr399Met | missense_variant | 7/7 | ENST00000669674.2 | |
PALM3 | NM_001367327.1 | c.998C>T | p.Thr333Met | missense_variant | 5/5 | ||
PALM3 | XM_047438763.1 | c.1115C>T | p.Thr372Met | missense_variant | 6/6 | ||
PALM3 | XM_047438764.1 | c.998C>T | p.Thr333Met | missense_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PALM3 | ENST00000669674.2 | c.1196C>T | p.Thr399Met | missense_variant | 7/7 | NM_001145028.2 | A2 | ||
PALM3 | ENST00000340790.9 | c.1151C>T | p.Thr384Met | missense_variant | 6/6 | 5 | P4 | ||
PALM3 | ENST00000661591.1 | c.1076C>T | p.Thr359Met | missense_variant | 4/4 | A2 | |||
PALM3 | ENST00000589048.2 | c.998C>T | p.Thr333Met | missense_variant | 5/5 | 3 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000659 AC: 10AN: 151752Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000287 AC: 45AN: 156754Hom.: 0 AF XY: 0.000350 AC XY: 29AN XY: 82838
GnomAD4 exome AF: 0.000143 AC: 200AN: 1399116Hom.: 0 Cov.: 34 AF XY: 0.000185 AC XY: 128AN XY: 690060
GnomAD4 genome ? AF: 0.0000658 AC: 10AN: 151868Hom.: 0 Cov.: 32 AF XY: 0.0000539 AC XY: 4AN XY: 74196
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 10, 2022 | The c.1151C>T (p.T384M) alteration is located in exon 6 (coding exon 6) of the PALM3 gene. This alteration results from a C to T substitution at nucleotide position 1151, causing the threonine (T) at amino acid position 384 to be replaced by a methionine (M). 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