chr5-78002861-T-C
Variant names:
Variant summary
Our verdict is Benign. The variant received -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBS1BS2
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
Publications
2 publications found
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]
AP3B1 Gene-Disease associations (from GenCC):
- Hermansky-Pudlak syndrome 2Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, ClinGen, G2P
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -18 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_multiple_submitters_no_conflicts, 2 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 the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
BS2
High Homozygotes in GnomAd4 at 14 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AP3B1 | NM_003664.5 | c.*41A>G | 3_prime_UTR_variant | Exon 27 of 27 | ENST00000255194.11 | NP_003655.3 | ||
AP3B1 | NM_001271769.2 | c.*41A>G | 3_prime_UTR_variant | Exon 27 of 27 | NP_001258698.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00886 AC: 1349AN: 152204Hom.: 14 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
1349
AN:
152204
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD2 exomes AF: 0.00905 AC: 2275AN: 251436 AF XY: 0.00896 show subpopulations
GnomAD2 exomes
AF:
AC:
2275
AN:
251436
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0118 AC: 17248AN: 1460972Hom.: 128 Cov.: 31 AF XY: 0.0116 AC XY: 8449AN XY: 726864 show subpopulations
GnomAD4 exome
AF:
AC:
17248
AN:
1460972
Hom.:
Cov.:
31
AF XY:
AC XY:
8449
AN XY:
726864
show subpopulations
African (AFR)
AF:
AC:
76
AN:
33456
American (AMR)
AF:
AC:
441
AN:
44724
Ashkenazi Jewish (ASJ)
AF:
AC:
574
AN:
26134
East Asian (EAS)
AF:
AC:
1
AN:
39686
South Asian (SAS)
AF:
AC:
419
AN:
86240
European-Finnish (FIN)
AF:
AC:
313
AN:
53418
Middle Eastern (MID)
AF:
AC:
35
AN:
5764
European-Non Finnish (NFE)
AF:
AC:
14696
AN:
1111186
Other (OTH)
AF:
AC:
693
AN:
60364
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.493
Heterozygous variant carriers
0
931
1863
2794
3726
4657
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.00886 AC: 1349AN: 152322Hom.: 14 Cov.: 32 AF XY: 0.00834 AC XY: 621AN XY: 74486 show subpopulations
GnomAD4 genome
AF:
AC:
1349
AN:
152322
Hom.:
Cov.:
32
AF XY:
AC XY:
621
AN XY:
74486
show subpopulations
African (AFR)
AF:
AC:
126
AN:
41562
American (AMR)
AF:
AC:
180
AN:
15294
Ashkenazi Jewish (ASJ)
AF:
AC:
90
AN:
3470
East Asian (EAS)
AF:
AC:
0
AN:
5192
South Asian (SAS)
AF:
AC:
19
AN:
4828
European-Finnish (FIN)
AF:
AC:
56
AN:
10618
Middle Eastern (MID)
AF:
AC:
2
AN:
294
European-Non Finnish (NFE)
AF:
AC:
855
AN:
68038
Other (OTH)
AF:
AC:
21
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
72
144
216
288
360
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
7
AN:
3478
ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
-
Breakthrough Genomics, Breakthrough Genomics
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:not provided
- -
Nov 10, 2018
GeneDx
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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