chr2-223765159-CCATCATCAT-C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BS2

The NM_001039569.2(AP1S3):​c.429+45_429+53delATGATGATG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000355 in 1,409,486 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)
Exomes 𝑓: 0.0000035 ( 0 hom. )

Consequence

AP1S3
NM_001039569.2 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.815
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 -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BS2
High AC in GnomAdExome4 at 5 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
AP1S3NM_001039569.2 linkc.429+45_429+53delATGATGATG intron_variant Intron 4 of 4 ENST00000396654.7 NP_001034658.1 Q96PC3-4
AP1S3XM_011510600.4 linkc.292-6418_292-6410delATGATGATG intron_variant Intron 3 of 3 XP_011508902.1
AP1S3NR_110905.2 linkn.600+45_600+53delATGATGATG intron_variant Intron 5 of 5
AP1S3NR_110906.2 linkn.452+45_452+53delATGATGATG 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+53delATGATGATG intron_variant Intron 4 of 4 2 NM_001039569.2 ENSP00000379891.2 Q96PC3-4
ENSG00000286239ENST00000650969.1 linkn.*1393+45_*1393+53delATGATGATG intron_variant Intron 16 of 16 ENSP00000498456.1 A0A494C0A6

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
AF:
0.00000355
AC:
5
AN:
1409486
Hom.:
0
AF XY:
0.00000285
AC XY:
2
AN XY:
700756
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000127
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000370
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
0

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