rs11989843

Positions:

• chr8-117138754-A-G

Variant summary

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

The ENST00000456015.7(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 ENST00000456015.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37

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 (AFR) allele frequency at 95% confidence interval = 0.277 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC30A8	NM_173851.3	c.71+3356A>G		intron_variant		ENST00000456015.7	NP_776250.2
LOC105375716	XR_007061067.1	n.819+33861T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC30A8	ENST00000456015.7	c.71+3356A>G		intron_variant		1	NM_173851.3	ENSP00000415011	P1

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

Gnomad4 AFR AF: 0.281

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.171

Gnomad4 EAS AF: 0.160

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.190

Gnomad4 OTH AF: 0.196

Alfa AF: 0.194 Hom.: 5062

Bravo AF: 0.214

Asia WGS AF: 0.116 AC: 404 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	2.5
DANN	Benign	0.69

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: rs11989843; hg19: chr8-118150993;