rs550499593
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The ENST00000507735.6(PALLD):āc.121C>Gā(p.Pro41Ala) variant causes a missense change. The variant allele was found at a frequency of 0.000431 in 1,497,448 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P41R) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000507735.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PALLD | NM_001166108.2 | c.1965-12910C>G | intron_variant | ENST00000505667.6 | NP_001159580.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PALLD | ENST00000505667.6 | c.1965-12910C>G | intron_variant | 1 | NM_001166108.2 | ENSP00000425556 | A2 |
Frequencies
GnomAD3 genomes AF: 0.000691 AC: 105AN: 151930Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00121 AC: 115AN: 94802Hom.: 0 AF XY: 0.00122 AC XY: 65AN XY: 53380
GnomAD4 exome AF: 0.000403 AC: 542AN: 1345410Hom.: 5 Cov.: 31 AF XY: 0.000432 AC XY: 287AN XY: 663666
GnomAD4 genome AF: 0.000684 AC: 104AN: 152038Hom.: 2 Cov.: 32 AF XY: 0.000861 AC XY: 64AN XY: 74330
ClinVar
Submissions by phenotype
Pancreatic adenocarcinoma Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 02, 2024 | - - |
PALLD-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 18, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at