rs6052399

Variant names:

• chr20-4146356-T-C
• rs6052399
• ENST00000493223.1:n.205+25172T>C

Your query was ambiguous. Multiple possible variants found:

• chr20-4146356-T-C
• chr20-4146356-T-G

Variant summary

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

The ENST00000493223.1(SMOX):​n.205+25172T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0879 in 152,198 control chromosomes in the GnomAD database, including 791 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 0.088 (791 hom., cov: 32)
• Consequence: SMOX ENST00000493223.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.216
• Publications: 3 publications found

Genes affected

SMOX (HGNC:15862): (spermine oxidase) Polyamines are ubiquitous polycationic alkylamines which include spermine, spermidine, putrescine, and agmatine. These molecules participate in a broad range of cellular functions which include cell cycle modulation, scavenging reactive oxygen species, and the control of gene expression. These molecules also play important roles in neurotransmission through their regulation of cell-surface receptor activity, involvement in intracellular signalling pathways, and their putative roles as neurotransmitters. This gene encodes an FAD-containing enzyme that catalyzes the oxidation of spermine to spermadine and secondarily produces hydrogen peroxide. Multiple transcript variants encoding different isoenzymes have been identified for this gene, some of which have failed to demonstrate significant oxidase activity on natural polyamine substrates. The characterized isoenzymes have distinctive biochemical characteristics and substrate specificities, suggesting the existence of additional levels of complexity in polyamine catabolism. [provided by RefSeq, Jul 2012]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000493223.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SMOX	ENST00000493223.1	TSL:3	n.205+25172T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0879 AC: 13369 AN: 152080 Hom.: 793 Cov.: 32

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.0717

Gnomad EAS AF: 0.0887

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.0523

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0423

Gnomad OTH AF: 0.0922

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

GnomAD4 genome AF: 0.0879 AC: 13384 AN: 152198 Hom.: 791 Cov.: 32 AF XY: 0.0890 AC XY: 6624 AN XY: 74410

African (AFR) AF: 0.159 AC: 6606 AN: 41526

American (AMR) AF: 0.117 AC: 1784 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0717 AC: 249 AN: 3472

East Asian (EAS) AF: 0.0889 AC: 459 AN: 5164

South Asian (SAS) AF: 0.132 AC: 638 AN: 4820

European-Finnish (FIN) AF: 0.0523 AC: 554 AN: 10600

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0423 AC: 2874 AN: 68008

Other (OTH) AF: 0.0907 AC: 192 AN: 2116

Alfa AF: 0.0524 Hom.: 333

Bravo AF: 0.0960

Asia WGS AF: 0.104 AC: 360 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.9
DANN	Benign	0.79
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs6052399; hg19: chr20-4127003;