rs7815720

Positions:

• chr8-117077274-G-A

Variant summary

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

The ENST00000521243.5(SLC30A8):​c.-106-69545G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,172 control chromosomes in the GnomAD database, including 1,165 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 0.12 (1165 hom., cov: 32)
• Consequence: SLC30A8 ENST00000521243.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.214

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 (EAS) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC30A8	NM_001172811.2	c.-106-69545G>A		intron_variant
SLC30A8	NM_001172813.2	c.-273-57958G>A		intron_variant
SLC30A8	NM_001172815.3	c.-226+38016G>A		intron_variant
SLC30A8	XM_024447083.2	c.-106-69545G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC30A8	ENST00000521243.5	c.-106-69545G>A		intron_variant		1
SLC30A8	ENST00000427715.2	c.-226+38016G>A		intron_variant		2
SLC30A8	ENST00000524274.5	c.-106-69545G>A		intron_variant		4
SLC30A8	ENST00000521035.5	n.295-57958G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18188 AN: 152054 Hom.: 1163 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.0362

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.120 AC: 18210 AN: 152172 Hom.: 1165 Cov.: 32 AF XY: 0.116 AC XY: 8657 AN XY: 74380

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.144

Gnomad4 SAS AF: 0.0367

Gnomad4 FIN AF: 0.111

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.103

Alfa AF: 0.121 Hom.: 579

Bravo AF: 0.119

Asia WGS AF: 0.0760 AC: 265 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	1.2
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7815720; hg19: chr8-118089513;