rs3019885

Variant names:

• chr8-117013406-T-A
• rs3019885
• ENST00000521243.5:c.-107+62287T>A

Your query was ambiguous. Multiple possible variants found:

• chr8-117013406-T-A
• chr8-117013406-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000521243.5(SLC30A8):​c.-107+62287T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: SLC30A8 ENST00000521243.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.556
• Publications: 45 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]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC30A8	NM_001172811.2	c.-107+62287T>A		intron_variant	Intron 2 of 9		NP_001166282.1
SLC30A8	NM_001172813.2	c.-274+6293T>A		intron_variant	Intron 2 of 10		NP_001166284.1
SLC30A8	NM_001172815.3	c.-265-25813T>A		intron_variant	Intron 1 of 10		NP_001166286.1
SLC30A8	XM_024447083.2	c.-107+62287T>A		intron_variant	Intron 1 of 8		XP_024302851.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC30A8	ENST00000521243.5	c.-107+62287T>A		intron_variant	Intron 2 of 9	1		ENSP00000428545.1
SLC30A8	ENST00000427715.2	c.-265-25813T>A		intron_variant	Intron 1 of 10	2		ENSP00000407505.2
SLC30A8	ENST00000524274.5	c.-107+62287T>A		intron_variant	Intron 2 of 4	4		ENSP00000427760.1
SLC30A8	ENST00000521035.5	n.294+6293T>A		intron_variant	Intron 2 of 4	4

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 53876

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	8.0
DANN	Benign	0.75
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs3019885; hg19: chr8-118025645;