chr5-78002861-T-C
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBS1BS2
The NM_003664.5(AP3B1):c.*41A>G variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.0115 in 1,613,294 control chromosomes in the GnomAD database, including 142 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0089 ( 14 hom., cov: 32)
Exomes 𝑓: 0.012 ( 128 hom. )
Consequence
AP3B1
NM_003664.5 3_prime_UTR
NM_003664.5 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.85
Genes affected
AP3B1 (HGNC:566): (adaptor related protein complex 3 subunit beta 1) This gene encodes a protein that may play a role in organelle biogenesis associated with melanosomes, platelet dense granules, and lysosomes. The encoded protein is part of the heterotetrameric AP-3 protein complex which interacts with the scaffolding protein clathrin. Mutations in this gene are associated with Hermansky-Pudlak syndrome type 2. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.45).
BP6
?
Variant 5-78002861-T-C is Benign according to our data. Variant chr5-78002861-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 1207984.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00886 (1349/152322) while in subpopulation NFE AF= 0.0126 (855/68038). AF 95% confidence interval is 0.0119. There are 14 homozygotes in gnomad4. There are 621 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 14 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AP3B1 | NM_003664.5 | c.*41A>G | 3_prime_UTR_variant | 27/27 | ENST00000255194.11 | ||
AP3B1 | NM_001271769.2 | c.*41A>G | 3_prime_UTR_variant | 27/27 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AP3B1 | ENST00000255194.11 | c.*41A>G | 3_prime_UTR_variant | 27/27 | 1 | NM_003664.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00886 AC: 1349AN: 152204Hom.: 14 Cov.: 32
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GnomAD3 exomes AF: 0.00905 AC: 2275AN: 251436Hom.: 19 AF XY: 0.00896 AC XY: 1217AN XY: 135884
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GnomAD4 exome AF: 0.0118 AC: 17248AN: 1460972Hom.: 128 Cov.: 31 AF XY: 0.0116 AC XY: 8449AN XY: 726864
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GnomAD4 genome ? AF: 0.00886 AC: 1349AN: 152322Hom.: 14 Cov.: 32 AF XY: 0.00834 AC XY: 621AN XY: 74486
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 10, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at