Variant NM_003664.5:c.*107T>A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_003664.5(AP3B1):c.*107T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 1,242,656 control chromosomes in the GnomAD database, including 41,333 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.29 ( 7471 hom., cov: 32)

Exomes 𝑓: 0.24 ( 33862 hom. )

Consequence

AP3B1
NM_003664.5 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 1.30

Variant links:

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.53).

BP6

Variant 5-78002795-A-T is Benign according to our data. Variant chr5-78002795-A-T is described in ClinVar as [Benign]. Clinvar id is 354217.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AP3B1	NM_003664.5 link	c.*107T>A		3_prime_UTR_variant	Exon 27 of 27	ENST00000255194.11	NP_003655.3	O00203-1A0A0S2Z5J4
AP3B1	NM_001271769.2 link	c.*107T>A		3_prime_UTR_variant	Exon 27 of 27		NP_001258698.1	O00203-3A0A0S2Z5J4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AP3B1	ENST00000255194 link	c.*107T>A		3_prime_UTR_variant	Exon 27 of 27	1	NM_003664.5	ENSP00000255194.7		O00203-1

Frequencies

GnomAD3 genomes

AF:

0.294

AC:

44715

AN:

152002

Hom.:

7440

Cov.:

show subpopulations

Gnomad AFR

AF:

0.426

Gnomad AMI

AF:

0.235

Gnomad AMR

AF:

0.415

Gnomad ASJ

AF:

0.166

Gnomad EAS

AF:

0.287

Gnomad SAS

AF:

0.181

Gnomad FIN

AF:

0.138

Gnomad MID

AF:

0.225

Gnomad NFE

AF:

0.227

Gnomad OTH

AF:

0.300

GnomAD4 exome

AF:

0.238

AC:

259595

AN:

1090536

Hom.:

33862

Cov.:

AF XY:

0.233

AC XY:

130487

AN XY:

559592

show subpopulations

Gnomad4 AFR exome

AF:

0.429

Gnomad4 AMR exome

AF:

0.457

Gnomad4 ASJ exome

AF:

0.175

Gnomad4 EAS exome

AF:

0.303

Gnomad4 SAS exome

AF:

0.173

Gnomad4 FIN exome

AF:

0.149

Gnomad4 NFE exome

AF:

0.231

Gnomad4 OTH exome

AF:

0.242

GnomAD4 genome

AF:

0.294

AC:

44796

AN:

152120

Hom.:

7471

Cov.:

AF XY:

0.292

AC XY:

21730

AN XY:

74366

show subpopulations

Gnomad4 AFR

AF:

0.426

Gnomad4 AMR

AF:

0.415

Gnomad4 ASJ

AF:

0.166

Gnomad4 EAS

AF:

0.287

Gnomad4 SAS

AF:

0.182

Gnomad4 FIN

AF:

0.138

Gnomad4 NFE

AF:

0.227

Gnomad4 OTH

AF:

0.303

Alfa

AF:

0.253

Hom.:

676

Bravo

AF:

0.321

Asia WGS

AF:

0.293

AC:

1020

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Nov 10, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

not specified

Benign:1

Nov 12, 2023

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is classified as Benign based on local population frequency. This variant was detected in 25% of patients studied by a panel of primary immunodeficiencies. Number of patients: 24. Only high quality variants are reported. -

Hermansky-Pudlak syndrome

Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.53

CADD

Benign

9.1

DANN

Benign

0.85

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over