rs6759518

chr2-27263727-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001318949.2(SLC30A3):c.80+283C>G variant causes a intron 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: SLC30A3 NM_001318949.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360

Genes affected

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC30A3	NM_001318949.2	c.80+283C>G		intron_variant
SLC30A3	NM_001318950.2	c.57-4793C>G		intron_variant
SLC30A3	NM_001318951.2	c.57-4793C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC30A3	ENST00000424577.5	c.-85-268C>G		intron_variant		5
SLC30A3	ENST00000426569.1	c.-53+283C>G		intron_variant		4
SLC30A3	ENST00000426924.5	c.57-4793C>G		intron_variant		5
SLC30A3	ENST00000432351.5	c.-53+283C>G		intron_variant		5

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

Gnomad4 AFR AF: 0.0800

Gnomad4 AMR AF: 0.0410

Gnomad4 ASJ AF: 0.0310

Gnomad4 EAS AF: 0.000791

Gnomad4 SAS AF: 0.0540

Gnomad4 FIN AF: 0.0321

Gnomad4 NFE AF: 0.0500

Gnomad4 OTH AF: 0.0546

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	6.1
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6759518; hg19: chr2-27486595;