rs10282940

chr8-117175587-G-A

Variant summary

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

The NM_173851.3(SLC30A8):c.*2906G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 152,108 control chromosomes in the GnomAD database, including 1,654 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 0.13 (1654 hom., cov: 33)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: SLC30A8 NM_173851.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.12

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC30A8	NM_173851.3	c.*2906G>A		3_prime_UTR_variant	8/8	ENST00000456015.7
LOC105375716	XR_007061067.1	n.560-2099C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC30A8	ENST00000456015.7	c.*2906G>A		3_prime_UTR_variant	8/8	1	NM_173851.3	P1
SLC30A8	ENST00000519688.5	c.*2906G>A		3_prime_UTR_variant	9/9	1
SLC30A8	ENST00000427715.2	c.*2906G>A		3_prime_UTR_variant	11/11	2

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20246 AN: 151986 Hom.: 1654 Cov.: 33

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.0104

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.0504

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0988

Gnomad OTH AF: 0.130

GnomAD4 exome AF: 0.250 AC: 1 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 NFE exome AF: 0.250

GnomAD4 genome AF: 0.133 AC: 20248 AN: 152104 Hom.: 1654 Cov.: 33 AF XY: 0.130 AC XY: 9645 AN XY: 74366

Gnomad4 AFR AF: 0.235

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.0105

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.0504

Gnomad4 NFE AF: 0.0988

Gnomad4 OTH AF: 0.129

Alfa AF: 0.104 Hom.: 1943

Bravo AF: 0.142

Asia WGS AF: 0.0790 AC: 275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	3.7
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10282940; hg19: chr8-118187826;