rs2466295

Variant names:

• chr8-117172802-C-T
• rs2466295
• NM_173851.3:c.*121C>T

Variant summary

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

The NM_173851.3(SLC30A8):​c.*121C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.621 in 1,127,406 control chromosomes in the GnomAD database, including 223,955 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 0.55 (24918 hom., cov: 33)
  • Exomes 𝑓: 0.63 (199037 hom.)
• Consequence: SLC30A8 NM_173851.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0820

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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC30A8	NM_173851.3	c.*121C>T		3_prime_UTR_variant	Exon 8 of 8	ENST00000456015.7	NP_776250.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC30A8	ENST00000456015.7	c.*121C>T		3_prime_UTR_variant	Exon 8 of 8	1	NM_173851.3	ENSP00000415011.2
SLC30A8	ENST00000519688.5	c.*121C>T		3_prime_UTR_variant	Exon 9 of 9	1		ENSP00000431069.1
SLC30A8	ENST00000427715.2	c.*121C>T		3_prime_UTR_variant	Exon 11 of 11	2		ENSP00000407505.2
SLC30A8	ENST00000521243.5	c.*121C>T		downstream_gene_variant		1		ENSP00000428545.1

Frequencies

GnomAD3 genomes AF: 0.546 AC: 82950 AN: 151910 Hom.: 24904 Cov.: 33

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.819

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.728

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.552

GnomAD4 exome AF: 0.633 AC: 617344 AN: 975378 Hom.: 199037 Cov.: 13 AF XY: 0.632 AC XY: 313810 AN XY: 496328

Gnomad4 AFR exome AF: 0.262

Gnomad4 AMR exome AF: 0.684

Gnomad4 ASJ exome AF: 0.591

Gnomad4 EAS exome AF: 0.832

Gnomad4 SAS exome AF: 0.609

Gnomad4 FIN exome AF: 0.711

Gnomad4 NFE exome AF: 0.632

Gnomad4 OTH exome AF: 0.611

GnomAD4 genome AF: 0.546 AC: 82991 AN: 152028 Hom.: 24918 Cov.: 33 AF XY: 0.555 AC XY: 41236 AN XY: 74308

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.639

Gnomad4 ASJ AF: 0.587

Gnomad4 EAS AF: 0.819

Gnomad4 SAS AF: 0.633

Gnomad4 FIN AF: 0.728

Gnomad4 NFE AF: 0.633

Gnomad4 OTH AF: 0.553

Alfa AF: 0.608 Hom.: 23150

Bravo AF: 0.530

Asia WGS AF: 0.645 AC: 2241 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.5
DANN	Benign	0.37

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: rs2466295; hg19: chr8-118185041; COSMIC: COSV69975536; COSMIC: COSV69975536;