rs11989843

Variant names:

• chr8-117138754-A-G
• rs11989843
• NM_173851.3:c.71+3356A>G

Variant summary

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

The NM_173851.3(SLC30A8):​c.71+3356A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 151,748 control chromosomes in the GnomAD database, including 3,463 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 0.21 (3463 hom., cov: 31)
• Consequence: SLC30A8 NM_173851.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37
• Publications: 5 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.277 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_173851.3. 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
	SLC30A8	NM_173851.3	MANE Select	c.71+3356A>G		intron	N/A	NP_776250.2
	SLC30A8	NM_001172811.2		c.-106-8065A>G		intron	N/A	NP_001166282.1
	SLC30A8	NM_001172813.2		c.-107+3356A>G		intron	N/A	NP_001166284.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC30A8	ENST00000456015.7	TSL:1 MANE Select	c.71+3356A>G		intron	N/A	ENSP00000415011.2
	SLC30A8	ENST00000519688.5	TSL:1	c.-107+3356A>G		intron	N/A	ENSP00000431069.1
	SLC30A8	ENST00000521243.5	TSL:1	c.-106-8065A>G		intron	N/A	ENSP00000428545.1

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31497 AN: 151628 Hom.: 3464 Cov.: 31

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.208 AC: 31517 AN: 151748 Hom.: 3463 Cov.: 31 AF XY: 0.203 AC XY: 15038 AN XY: 74170

African (AFR) AF: 0.281 AC: 11640 AN: 41384

American (AMR) AF: 0.181 AC: 2760 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 593 AN: 3466

East Asian (EAS) AF: 0.160 AC: 820 AN: 5110

South Asian (SAS) AF: 0.103 AC: 495 AN: 4810

European-Finnish (FIN) AF: 0.155 AC: 1644 AN: 10586

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.190 AC: 12919 AN: 67864

Other (OTH) AF: 0.196 AC: 412 AN: 2102

Alfa AF: 0.201 Hom.: 9209

Bravo AF: 0.214

Asia WGS AF: 0.116 AC: 404 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.5
DANN	Benign	0.69
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11989843; hg19: chr8-118150993;