5-115894028-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001284.4(AP3S1):​c.274-1059G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 151,966 control chromosomes in the GnomAD database, including 4,184 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.22 ( 4184 hom., cov: 32)

Consequence

AP3S1
NM_001284.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.802
Variant links:
Genes affected
AP3S1 (HGNC:2013): (adaptor related protein complex 3 subunit sigma 1) This gene encodes a subunit of the AP3 adaptor complex. This complex functions in the formation of subcellular vesicles budded from the Golgi body. Several related pseudogenes of this gene have been found. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
AP3S1NM_001284.4 linkuse as main transcriptc.274-1059G>A intron_variant ENST00000316788.12

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
AP3S1ENST00000316788.12 linkuse as main transcriptc.274-1059G>A intron_variant 1 NM_001284.4 P1

Frequencies

GnomAD3 genomes
AF:
0.218
AC:
33170
AN:
151848
Hom.:
4170
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.328
Gnomad AMI
AF:
0.224
Gnomad AMR
AF:
0.164
Gnomad ASJ
AF:
0.218
Gnomad EAS
AF:
0.00328
Gnomad SAS
AF:
0.0730
Gnomad FIN
AF:
0.183
Gnomad MID
AF:
0.215
Gnomad NFE
AF:
0.196
Gnomad OTH
AF:
0.225
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.219
AC:
33222
AN:
151966
Hom.:
4184
Cov.:
32
AF XY:
0.214
AC XY:
15915
AN XY:
74280
show subpopulations
Gnomad4 AFR
AF:
0.329
Gnomad4 AMR
AF:
0.164
Gnomad4 ASJ
AF:
0.218
Gnomad4 EAS
AF:
0.00309
Gnomad4 SAS
AF:
0.0733
Gnomad4 FIN
AF:
0.183
Gnomad4 NFE
AF:
0.196
Gnomad4 OTH
AF:
0.223
Alfa
AF:
0.195
Hom.:
6252
Bravo
AF:
0.225
Asia WGS
AF:
0.0640
AC:
226
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
0.12
DANN
Benign
0.21

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.

Other links and lift over

dbSNP: rs6882704; hg19: chr5-115229725; COSMIC: COSV57473990; COSMIC: COSV57473990; API