5-78015546-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_003664.5(AP3B1):c.2995G>A(p.Val999Met) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00685 in 1,613,418 control chromosomes in the GnomAD database, including 64 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_003664.5 missense, splice_region
Scores
Clinical Significance
Conservation
Genome browser will be placed here
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.2995G>A | p.Val999Met | missense_variant, splice_region_variant | 26/27 | ENST00000255194.11 | |
AP3B1 | NM_001271769.2 | c.2848G>A | p.Val950Met | missense_variant, splice_region_variant | 26/27 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AP3B1 | ENST00000255194.11 | c.2995G>A | p.Val999Met | missense_variant, splice_region_variant | 26/27 | 1 | NM_003664.5 | P2 |
Frequencies
GnomAD3 genomes AF: 0.00499 AC: 759AN: 152048Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.00413 AC: 1038AN: 251256Hom.: 5 AF XY: 0.00416 AC XY: 565AN XY: 135808
GnomAD4 exome AF: 0.00704 AC: 10291AN: 1461252Hom.: 61 Cov.: 30 AF XY: 0.00683 AC XY: 4963AN XY: 726898
GnomAD4 genome AF: 0.00499 AC: 759AN: 152166Hom.: 3 Cov.: 32 AF XY: 0.00480 AC XY: 357AN XY: 74404
ClinVar
Submissions by phenotype
not specified Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Oct 14, 2016 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | May 08, 2015 | - - |
Hermansky-Pudlak syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Hermansky-Pudlak syndrome 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2024 | AP3B1: BP4, BS2 - |
Autoinflammatory syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Aug 17, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at