rs2938864

chr8-117000026-G-Achr8-117000026-G-T

Variant summary

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

The ENST00000521243.5(SLC30A8):c.-107+48907G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 151,892 control chromosomes in the GnomAD database, including 11,944 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 0.38 (11944 hom., cov: 31)
• Consequence: SLC30A8 ENST00000521243.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.414

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]

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 (AMR) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC30A8	NM_001172811.2	c.-107+48907G>A		intron_variant
SLC30A8	NM_001172813.2	c.-396-6965G>A		intron_variant
SLC30A8	NM_001172815.3	c.-265-39193G>A		intron_variant
SLC30A8	XM_024447083.2	c.-107+48907G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC30A8	ENST00000521243.5	c.-107+48907G>A		intron_variant		1
SLC30A8	ENST00000427715.2	c.-265-39193G>A		intron_variant		2
SLC30A8	ENST00000524274.5	c.-107+48907G>A		intron_variant		4
SLC30A8	ENST00000521035.5	n.172-6965G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.380 AC: 57609 AN: 151774 Hom.: 11933 Cov.: 31

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.379 AC: 57638 AN: 151892 Hom.: 11944 Cov.: 31 AF XY: 0.380 AC XY: 28234 AN XY: 74224

Gnomad4 AFR AF: 0.212

Gnomad4 AMR AF: 0.504

Gnomad4 ASJ AF: 0.366

Gnomad4 EAS AF: 0.279

Gnomad4 SAS AF: 0.492

Gnomad4 FIN AF: 0.350

Gnomad4 NFE AF: 0.457

Gnomad4 OTH AF: 0.405

Alfa AF: 0.439 Hom.: 6990

Bravo AF: 0.380

Asia WGS AF: 0.345 AC: 1199 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	0.64
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2938864; hg19: chr8-118012265;