rs6759518

Variant names:

• chr2-27263727-G-C
• rs6759518
• ENST00000720716.1:n.420G>C

Variant summary

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

The ENST00000720716.1(ENSG00000294052):​n.420G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0545 in 149,040 control chromosomes in the GnomAD database, including 252 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 0.055 (252 hom., cov: 29)
• Consequence: ENSG00000294052 ENST00000720716.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360
• Publications: 7 publications found

Genes affected

ENSG00000294052 (HGNC:):

SLC30A3 (HGNC:11014): (solute carrier family 30 member 3) Predicted to enable zinc ion transmembrane transporter activity. Involved in regulation of sequestering of zinc ion. Located in late endosome and synaptic vesicle. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0777 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000720716.1. 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
	SLC30A3	NM_001318949.2		c.80+283C>G		intron	N/A	NP_001305878.1
	SLC30A3	NM_001318950.2		c.57-4793C>G		intron	N/A	NP_001305879.1
	SLC30A3	NM_001318951.2		c.57-4793C>G		intron	N/A	NP_001305880.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000294052	ENST00000720716.1		n.420G>C		non_coding_transcript_exon	Exon 2 of 2
	SLC30A3	ENST00000432351.5	TSL:5	c.-53+283C>G		intron	N/A	ENSP00000414320.1
	SLC30A3	ENST00000426924.5	TSL:5	c.57-4793C>G		intron	N/A	ENSP00000393545.1

Frequencies

GnomAD3 genomes AF: 0.0546 AC: 8133 AN: 148924 Hom.: 252 Cov.: 29

Gnomad AFR AF: 0.0803

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.0410

Gnomad ASJ AF: 0.0310

Gnomad EAS AF: 0.000790

Gnomad SAS AF: 0.0534

Gnomad FIN AF: 0.0321

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0501

Gnomad OTH AF: 0.0552

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

GnomAD4 genome AF: 0.0545 AC: 8129 AN: 149040 Hom.: 252 Cov.: 29 AF XY: 0.0529 AC XY: 3838 AN XY: 72540

African (AFR) AF: 0.0800 AC: 3237 AN: 40452

American (AMR) AF: 0.0410 AC: 602 AN: 14686

Ashkenazi Jewish (ASJ) AF: 0.0310 AC: 107 AN: 3456

East Asian (EAS) AF: 0.000791 AC: 4 AN: 5054

South Asian (SAS) AF: 0.0540 AC: 236 AN: 4372

European-Finnish (FIN) AF: 0.0321 AC: 331 AN: 10320

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0500 AC: 3376 AN: 67484

Other (OTH) AF: 0.0546 AC: 110 AN: 2014

Alfa AF: 0.0549 Hom.: 33

Bravo AF: 0.0574

Asia WGS AF: 0.0240 AC: 82 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.1
DANN	Benign	0.57
PhyloP100		-0.036
PromoterAI		0.037	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs6759518; hg19: chr2-27486595;