rs201995410
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002579.3(PALM):c.71G>A(p.Arg24Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00111 in 1,194,832 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_002579.3 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PALM | NM_002579.3 | c.71G>A | p.Arg24Gln | missense_variant | 3/9 | ENST00000338448.10 | NP_002570.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PALM | ENST00000338448.10 | c.71G>A | p.Arg24Gln | missense_variant | 3/9 | 1 | NM_002579.3 | ENSP00000341911.4 |
Frequencies
GnomAD3 genomes AF: 0.000529 AC: 76AN: 143584Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.000416 AC: 61AN: 146634Hom.: 0 AF XY: 0.000484 AC XY: 38AN XY: 78552
GnomAD4 exome AF: 0.00119 AC: 1249AN: 1051104Hom.: 0 Cov.: 30 AF XY: 0.00114 AC XY: 592AN XY: 520318
GnomAD4 genome AF: 0.000529 AC: 76AN: 143728Hom.: 0 Cov.: 30 AF XY: 0.000629 AC XY: 44AN XY: 69956
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 09, 2021 | The c.71G>A (p.R24Q) alteration is located in exon 3 (coding exon 3) of the PALM gene. This alteration results from a G to A substitution at nucleotide position 71, causing the arginine (R) at amino acid position 24 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
atypical cerebral palsy Uncertain:1
Uncertain significance, criteria provided, single submitter | research | TIDEX, University of British Columbia | - | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jul 03, 2023 | This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 24 of the PALM protein (p.Arg24Gln). This variant is present in population databases (rs201995410, gnomAD 0.1%), and has an allele count higher than expected for a pathogenic variant. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. ClinVar contains an entry for this variant (Variation ID: 431724). This missense change has been observed in individual(s) with loss or impairment of motor function (PMID: 30542205). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at