dbSNP rs6469675: SLC30A8:c.272-34A>G (chr8-117152910-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_173851.3(SLC30A8):c.272-34A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 1,456,850 control chromosomes in the GnomAD database, including 71,357 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 0.39 ( 14256 hom., cov: 32)

Exomes 𝑓: 0.29 ( 57101 hom. )

Consequence

SLC30A8
NM_173851.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.645

Publications

12 publications found

Variant links:

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]

SLC30A8 links:

LOC105375716 (HGNC:):

LOC105375716 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC30A8	NM_173851.3 link	c.272-34A>G		intron_variant	Intron 2 of 7	ENST00000456015.7	NP_776250.2	Q8IWU4-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC30A8	ENST00000456015.7 link	c.272-34A>G		intron_variant	Intron 2 of 7	1	NM_173851.3	ENSP00000415011.2		Q8IWU4-1

Frequencies

GnomAD3 genomes

AF:

0.385

AC:

58440

AN:

151820

Hom.:

14211

Cov.:

show subpopulations

Gnomad AFR

AF:

0.695

Gnomad AMI

AF:

0.229

Gnomad AMR

AF:

0.283

Gnomad ASJ

AF:

0.265

Gnomad EAS

AF:

0.351

Gnomad SAS

AF:

0.282

Gnomad FIN

AF:

0.203

Gnomad MID

AF:

0.272

Gnomad NFE

AF:

0.268

Gnomad OTH

AF:

0.346

GnomAD2 exomes

AF:

0.305

AC:

61828

AN:

202860

AF XY:

0.297

show subpopulations

Gnomad AFR exome

AF:

0.705

Gnomad AMR exome

AF:

0.226

Gnomad ASJ exome

AF:

0.271

Gnomad EAS exome

AF:

0.380

Gnomad FIN exome

AF:

0.215

Gnomad NFE exome

AF:

0.274

Gnomad OTH exome

AF:

0.289

GnomAD4 exome

AF:

0.285

AC:

371939

AN:

1304912

Hom.:

57101

Cov.:

AF XY:

0.284

AC XY:

180956

AN XY:

637736

show subpopulations

African (AFR)

AF:

0.709

AC:

21704

AN:

30626

American (AMR)

AF:

0.233

AC:

8124

AN:

34892

Ashkenazi Jewish (ASJ)

AF:

0.268

AC:

5502

AN:

20538

East Asian (EAS)

AF:

0.333

AC:

12219

AN:

36748

South Asian (SAS)

AF:

0.281

AC:

16558

AN:

58954

European-Finnish (FIN)

AF:

0.221

AC:

10448

AN:

47322

Middle Eastern (MID)

AF:

0.280

AC:

1438

AN:

5128

European-Non Finnish (NFE)

AF:

0.275

AC:

279797

AN:

1017584

Other (OTH)

AF:

0.304

AC:

16149

AN:

53120

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.467

Heterozygous variant carriers

10409

20818

31228

41637

52046

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.385

AC:

58545

AN:

151938

Hom.:

14256

Cov.:

AF XY:

0.378

AC XY:

28093

AN XY:

74248

show subpopulations

African (AFR)

AF:

0.695

AC:

28785

AN:

41404

American (AMR)

AF:

0.283

AC:

4321

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.265

AC:

918

AN:

3468

East Asian (EAS)

AF:

0.351

AC:

1809

AN:

5148

South Asian (SAS)

AF:

0.282

AC:

1348

AN:

4782

European-Finnish (FIN)

AF:

0.203

AC:

2146

AN:

10594

Middle Eastern (MID)

AF:

0.286

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.268

AC:

18195

AN:

67944

Other (OTH)

AF:

0.346

AC:

731

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1563

3126

4690

6253

7816

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.287

Hom.:

7126

Bravo

AF:

0.404

Asia WGS

AF:

0.368

AC:

1281

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.63

(source)

DANN

Benign

0.84

PhyloP100

-0.65

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

Details are displayed if max score is > 0.2

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

Publications

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rs6469675

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over