rs4876369

chr8-117151265-A-G

Variant summary

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

The NM_173851.3(SLC30A8):c.272-1679A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 152,238 control chromosomes in the GnomAD database, including 994 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 0.10 (994 hom., cov: 32)
• Consequence: SLC30A8 NM_173851.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.797

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.142 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC30A8	NM_173851.3	c.272-1679A>G		intron_variant		ENST00000456015.7
LOC105375716	XR_007061067.1	n.819+21350T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC30A8	ENST00000456015.7	c.272-1679A>G		intron_variant		1	NM_173851.3	P1

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15552 AN: 152120 Hom.: 994 Cov.: 32

Gnomad AFR AF: 0.0321

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.0324

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.0943

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

GnomAD4 genome AF: 0.102 AC: 15558 AN: 152238 Hom.: 994 Cov.: 32 AF XY: 0.0993 AC XY: 7388 AN XY: 74434

Gnomad4 AFR AF: 0.0321

Gnomad4 AMR AF: 0.101

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.146

Gnomad4 SAS AF: 0.0330

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.144

Gnomad4 OTH AF: 0.0938

Alfa AF: 0.112 Hom.: 132

Bravo AF: 0.0983

Asia WGS AF: 0.0680 AC: 234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.24
Dann	Benign	0.44

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: rs4876369; hg19: chr8-118163504; COSMIC: COSV69975344; COSMIC: COSV69975344;