Genetic Variant SLC30A8:c.*1018A>G (chr8-117173699-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.*1018A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 152,036 control chromosomes in the GnomAD database, including 9,555 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 0.34 ( 9554 hom., cov: 32)

Exomes 𝑓: 0.58 ( 1 hom. )

Consequence

SLC30A8
NM_173851.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.62

Publications

36 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=-0.92).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.426 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC30A8	NM_173851.3 link	c.*1018A>G		3_prime_UTR_variant	Exon 8 of 8	ENST00000456015.7	NP_776250.2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
SLC30A8	ENST00000456015.7 link	c.*1018A>G	3_prime_UTR_variant	Exon 8 of 8	1	NM_173851.3	ENSP00000415011.2
SLC30A8	ENST00000519688.5 link	c.*1018A>G	3_prime_UTR_variant	Exon 9 of 9	1		ENSP00000431069.1
SLC30A8	ENST00000427715.2 link	c.*1018A>G	3_prime_UTR_variant	Exon 11 of 11	2		ENSP00000407505.2

Frequencies

GnomAD3 genomes

AF:

0.338

AC:

51335

AN:

151906

Hom.:

9551

Cov.:

show subpopulations

Gnomad AFR

AF:

0.180

Gnomad AMI

AF:

0.502

Gnomad AMR

AF:

0.410

Gnomad ASJ

AF:

0.360

Gnomad EAS

AF:

0.363

Gnomad SAS

AF:

0.443

Gnomad FIN

AF:

0.414

Gnomad MID

AF:

0.421

Gnomad NFE

AF:

0.393

Gnomad OTH

AF:

0.321

GnomAD4 exome

AF:

0.583

AC:

AN:

Hom.:

Cov.:

AF XY:

0.583

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.583

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.555

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.338

AC:

51351

AN:

152024

Hom.:

9554

Cov.:

AF XY:

0.341

AC XY:

25322

AN XY:

74294

show subpopulations

African (AFR)

AF:

0.180

AC:

7470

AN:

41520

American (AMR)

AF:

0.411

AC:

6273

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.360

AC:

1244

AN:

3460

East Asian (EAS)

AF:

0.364

AC:

1873

AN:

5146

South Asian (SAS)

AF:

0.442

AC:

2135

AN:

4830

European-Finnish (FIN)

AF:

0.414

AC:

4370

AN:

10548

Middle Eastern (MID)

AF:

0.415

AC:

122

AN:

294

European-Non Finnish (NFE)

AF:

0.393

AC:

26723

AN:

67942

Other (OTH)

AF:

0.325

AC:

684

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1683

3367

5050

6734

8417

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

518

1036

1554

2072

2590

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.373

Hom.:

33091

Bravo

AF:

0.328

Asia WGS

AF:

0.367

AC:

1280

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.018

(source)

DANN

Benign

0.34

PhyloP100

-1.6

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over