8-117110827-C-G

Position:

• chr8-117110827-C-G

Variant summary

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

The XR_007061067.1(LOC105375716):​n.820-24158G>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 152,074 control chromosomes in the GnomAD database, including 1,246 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 0.11 (1246 hom., cov: 32)
• Consequence: LOC105375716 XR_007061067.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.318

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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375716	XR_007061067.1	n.820-24158G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC30A8	ENST00000521243.5	c.-106-35992C>G		intron_variant		1		ENSP00000428545
SLC30A8	ENST00000427715.2	c.-225-24453C>G		intron_variant		2		ENSP00000407505
SLC30A8	ENST00000524274.5	c.-106-35992C>G		intron_variant		4		ENSP00000427760
SLC30A8	ENST00000521035.5	n.295-24405C>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17233 AN: 151958 Hom.: 1246 Cov.: 32

Gnomad AFR AF: 0.0349

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.0332

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.113 AC: 17249 AN: 152074 Hom.: 1246 Cov.: 32 AF XY: 0.111 AC XY: 8215 AN XY: 74322

Gnomad4 AFR AF: 0.0352

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.141

Gnomad4 EAS AF: 0.146

Gnomad4 SAS AF: 0.0339

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.103

Alfa AF: 0.129 Hom.: 165

Bravo AF: 0.107

Asia WGS AF: 0.0700 AC: 244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.9
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13269119; hg19: chr8-118123066;