rs139344924
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_003664.5(AP3B1):c.2661C>A(p.Phe887Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0102 in 1,614,086 control chromosomes in the GnomAD database, including 110 homozygotes. 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_003664.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AP3B1 | NM_003664.5 | c.2661C>A | p.Phe887Leu | missense_variant | 23/27 | ENST00000255194.11 | |
AP3B1 | NM_001271769.2 | c.2514C>A | p.Phe838Leu | missense_variant | 23/27 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AP3B1 | ENST00000255194.11 | c.2661C>A | p.Phe887Leu | missense_variant | 23/27 | 1 | NM_003664.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00694 AC: 1056AN: 152142Hom.: 5 Cov.: 32
GnomAD3 exomes AF: 0.00774 AC: 1947AN: 251458Hom.: 17 AF XY: 0.00819 AC XY: 1113AN XY: 135904
GnomAD4 exome AF: 0.0105 AC: 15376AN: 1461826Hom.: 105 Cov.: 32 AF XY: 0.0105 AC XY: 7618AN XY: 727214
GnomAD4 genome ? AF: 0.00694 AC: 1056AN: 152260Hom.: 5 Cov.: 32 AF XY: 0.00647 AC XY: 482AN XY: 74444
ClinVar
Submissions by phenotype
not specified Benign:3
Benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Feb 21, 2013 | Phe887Leu in exon 23 of AP3B1: This variant is not expected to have clinical sig nificance because it has been identified in 1.2% (99/8600) of European American chromosomes from a broad population by the NHLBI Exome Sequencing Project (http: //evs.gs.washington.edu/EVS; dbSNP rs139344924). - |
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jul 28, 2015 | - - |
Hermansky-Pudlak syndrome 2 Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Johns Hopkins Genomics, Johns Hopkins University | Mar 20, 2019 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2024 | AP3B1: BP4, BS1, BS2 - |
Likely benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Hermansky-Pudlak syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Autoinflammatory syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Feb 05, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at