rs2466293

chr8-117173699-A-G

Variant summary

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

The NM_173851.3(SLC30A8):c.*1018A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 152,036 control chromosomes in the GnomAD database, including 9,555 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 0.34 (9554 hom., cov: 32)
  • Exomes 𝑓: 0.58 (1 hom.)
• Consequence: SLC30A8 NM_173851.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62

Genes affected

SLC30A8 (HGNC:20303): (solute carrier family 30 member 8) The protein encoded by this gene is a zinc efflux transporter involved in the accumulation of zinc in intracellular vesicles. This gene is expressed at a high level only in the pancreas, particularly in islets of Langerhans. The encoded protein colocalizes with insulin in the secretory pathway granules of the insulin-secreting INS-1 cells. Allelic variants of this gene exist that confer susceptibility to diabetes mellitus, noninsulin-dependent (NIDDM). Several transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Mar 2010]

LOC105375716 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.426 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC30A8	NM_173851.3	c.*1018A>G		3_prime_UTR_variant	8/8	ENST00000456015.7
LOC105375716	XR_007061067.1	n.560-211T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC30A8	ENST00000456015.7	c.*1018A>G		3_prime_UTR_variant	8/8	1	NM_173851.3	P1
SLC30A8	ENST00000519688.5	c.*1018A>G		3_prime_UTR_variant	9/9	1
SLC30A8	ENST00000427715.2	c.*1018A>G		3_prime_UTR_variant	11/11	2

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51335 AN: 151906 Hom.: 9551 Cov.: 32

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.321

GnomAD4 exome AF: 0.583 AC: 7 AN: 12 Hom.: 1 Cov.: 0 AF XY: 0.583 AC XY: 7 AN XY: 12

Gnomad4 NFE exome AF: 0.583

GnomAD4 genome AF: 0.338 AC: 51351 AN: 152024 Hom.: 9554 Cov.: 32 AF XY: 0.341 AC XY: 25322 AN XY: 74294

Gnomad4 AFR AF: 0.180

Gnomad4 AMR AF: 0.411

Gnomad4 ASJ AF: 0.360

Gnomad4 EAS AF: 0.364

Gnomad4 SAS AF: 0.442

Gnomad4 FIN AF: 0.414

Gnomad4 NFE AF: 0.393

Gnomad4 OTH AF: 0.325

Alfa AF: 0.382 Hom.: 15363

Bravo AF: 0.328

Asia WGS AF: 0.367 AC: 1280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.018
Dann	Benign	0.34

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

Other links and lift over

dbSNP: rs2466293; hg19: chr8-118185938;