NM_001039569.2:c.429+45_429+53dupATGATGATG

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_001039569.2(AP1S3):​c.429+45_429+53dupATGATGATG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0037 in 1,560,316 control chromosomes in the GnomAD database, including 22 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0032 ( 1 hom., cov: 0)
Exomes 𝑓: 0.0038 ( 21 hom. )

Consequence

AP1S3
NM_001039569.2 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.488
Variant links:
Genes affected
AP1S3 (HGNC:18971): (adaptor related protein complex 1 subunit sigma 3) This gene encodes a member of the adaptor-related protein complex 1, sigma subunit genes. The encoded protein is a component of adaptor protein complex 1 (AP-1), one of the AP complexes involved in claathrin-mediated vesicular transport from the Golgi or endosomes. Disruption of the pathway for display of HIV-1 antigens, which prevents recognition of the virus by cytotoxic T cells, has been shown to involve the AP-1 complex (PMID: 15569716). Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2014]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BS2
High AC in GnomAd4 at 481 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
AP1S3NM_001039569.2 linkc.429+45_429+53dupATGATGATG intron_variant Intron 4 of 4 ENST00000396654.7 NP_001034658.1 Q96PC3-4
AP1S3XM_011510600.4 linkc.292-6418_292-6410dupATGATGATG intron_variant Intron 3 of 3 XP_011508902.1
AP1S3NR_110905.2 linkn.600+45_600+53dupATGATGATG intron_variant Intron 5 of 5
AP1S3NR_110906.2 linkn.452+45_452+53dupATGATGATG intron_variant Intron 3 of 3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
AP1S3ENST00000396654.7 linkc.429+45_429+53dupATGATGATG intron_variant Intron 4 of 4 2 NM_001039569.2 ENSP00000379891.2 Q96PC3-4
ENSG00000286239ENST00000650969.1 linkn.*1393+45_*1393+53dupATGATGATG intron_variant Intron 16 of 16 ENSP00000498456.1 A0A494C0A6

Frequencies

GnomAD3 genomes
AF:
0.00319
AC:
482
AN:
150902
Hom.:
1
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.00154
Gnomad AMI
AF:
0.00221
Gnomad AMR
AF:
0.00516
Gnomad ASJ
AF:
0.00405
Gnomad EAS
AF:
0.000389
Gnomad SAS
AF:
0.00190
Gnomad FIN
AF:
0.00105
Gnomad MID
AF:
0.00949
Gnomad NFE
AF:
0.00424
Gnomad OTH
AF:
0.00626
GnomAD3 exomes
AF:
0.00340
AC:
686
AN:
201824
Hom.:
9
AF XY:
0.00356
AC XY:
392
AN XY:
109964
show subpopulations
Gnomad AFR exome
AF:
0.00103
Gnomad AMR exome
AF:
0.00267
Gnomad ASJ exome
AF:
0.00281
Gnomad EAS exome
AF:
0.000795
Gnomad SAS exome
AF:
0.00217
Gnomad FIN exome
AF:
0.00128
Gnomad NFE exome
AF:
0.00491
Gnomad OTH exome
AF:
0.00506
GnomAD4 exome
AF:
0.00375
AC:
5291
AN:
1409294
Hom.:
21
Cov.:
32
AF XY:
0.00377
AC XY:
2643
AN XY:
700672
show subpopulations
Gnomad4 AFR exome
AF:
0.00169
Gnomad4 AMR exome
AF:
0.00312
Gnomad4 ASJ exome
AF:
0.00224
Gnomad4 EAS exome
AF:
0.000490
Gnomad4 SAS exome
AF:
0.00209
Gnomad4 FIN exome
AF:
0.00185
Gnomad4 NFE exome
AF:
0.00410
Gnomad4 OTH exome
AF:
0.00427
GnomAD4 genome
AF:
0.00318
AC:
481
AN:
151022
Hom.:
1
Cov.:
0
AF XY:
0.00311
AC XY:
229
AN XY:
73736
show subpopulations
Gnomad4 AFR
AF:
0.00153
Gnomad4 AMR
AF:
0.00522
Gnomad4 ASJ
AF:
0.00405
Gnomad4 EAS
AF:
0.000390
Gnomad4 SAS
AF:
0.00169
Gnomad4 FIN
AF:
0.00105
Gnomad4 NFE
AF:
0.00423
Gnomad4 OTH
AF:
0.00618

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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.

Other links and lift over

dbSNP: rs10644138; hg19: chr2-224629876; API