rs3797568

Variant names:

• chr5-115875527-A-G
• rs3797568
• NM_001284.4:c.273+5399A>G

Your query was ambiguous. Multiple possible variants found:

• chr5-115875527-A-G
• chr5-115875527-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001284.4(AP3S1):​c.273+5399A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.376 in 152,004 control chromosomes in the GnomAD database, including 11,241 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 0.38 (11241 hom., cov: 32)
• Consequence: AP3S1 NM_001284.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.524
• Publications: 3 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AP3S1	NM_001284.4	c.273+5399A>G		intron_variant	Intron 3 of 5	ENST00000316788.12	NP_001275.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AP3S1	ENST00000316788.12	c.273+5399A>G		intron_variant	Intron 3 of 5	1	NM_001284.4	ENSP00000325369.7

Frequencies

GnomAD3 genomes AF: 0.376 AC: 57057 AN: 151886 Hom.: 11213 Cov.: 32

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.382

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.376 AC: 57146 AN: 152004 Hom.: 11241 Cov.: 32 AF XY: 0.379 AC XY: 28140 AN XY: 74294

African (AFR) AF: 0.454 AC: 18806 AN: 41448

American (AMR) AF: 0.456 AC: 6960 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 1168 AN: 3470

East Asian (EAS) AF: 0.331 AC: 1705 AN: 5158

South Asian (SAS) AF: 0.342 AC: 1648 AN: 4816

European-Finnish (FIN) AF: 0.345 AC: 3646 AN: 10570

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.324 AC: 22051 AN: 67964

Other (OTH) AF: 0.380 AC: 800 AN: 2108

Alfa AF: 0.340 Hom.: 6690

Bravo AF: 0.388

Asia WGS AF: 0.328 AC: 1142 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.48
PhyloP100		-0.52
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3797568; hg19: chr5-115211224; COSMIC: COSV57473859;