dbSNP rs3802177: SLC30A8:c.*105G>A (chr8-117172786-G-A) – 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.*105G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 1,327,950 control chromosomes in the GnomAD database, including 59,489 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 0.25 ( 5605 hom., cov: 33)

Exomes 𝑓: 0.30 ( 53884 hom. )

Consequence

SLC30A8
NM_173851.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.44

Publications

171 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:

Genome browser will be placed here

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=-0.82).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC30A8	NM_173851.3 link	c.*105G>A		3_prime_UTR_variant	Exon 8 of 8	ENST00000456015.7	NP_776250.2	Q8IWU4-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
SLC30A8	ENST00000456015.7 link	c.*105G>A	3_prime_UTR_variant	Exon 8 of 8	1	NM_173851.3	ENSP00000415011.2	Q8IWU4-1
SLC30A8	ENST00000519688.5 link	c.*105G>A	3_prime_UTR_variant	Exon 9 of 9	1		ENSP00000431069.1	Q8IWU4-2
SLC30A8	ENST00000521243.5 link	c.*105G>A	3_prime_UTR_variant	Exon 10 of 10	1		ENSP00000428545.1	Q8IWU4-2
SLC30A8	ENST00000427715.2 link	c.*105G>A	3_prime_UTR_variant	Exon 11 of 11	2		ENSP00000407505.2	Q8IWU4-2

Frequencies

GnomAD3 genomes

AF:

0.249

AC:

37793

AN:

151974

Hom.:

5603

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0942

Gnomad AMI

AF:

0.170

Gnomad AMR

AF:

0.249

Gnomad ASJ

AF:

0.269

Gnomad EAS

AF:

0.456

Gnomad SAS

AF:

0.232

Gnomad FIN

AF:

0.399

Gnomad MID

AF:

0.231

Gnomad NFE

AF:

0.305

Gnomad OTH

AF:

0.255

GnomAD4 exome

AF:

0.296

AC:

347970

AN:

1175858

Hom.:

53884

Cov.:

AF XY:

0.295

AC XY:

174482

AN XY:

591392

show subpopulations

African (AFR)

AF:

0.0799

AC:

2133

AN:

26708

American (AMR)

AF:

0.248

AC:

8378

AN:

33758

Ashkenazi Jewish (ASJ)

AF:

0.264

AC:

5510

AN:

20844

East Asian (EAS)

AF:

0.437

AC:

16597

AN:

37980

South Asian (SAS)

AF:

0.230

AC:

16431

AN:

71362

European-Finnish (FIN)

AF:

0.377

AC:

18924

AN:

50142

Middle Eastern (MID)

AF:

0.196

AC:

984

AN:

5014

European-Non Finnish (NFE)

AF:

0.301

AC:

264560

AN:

879498

Other (OTH)

AF:

0.286

AC:

14453

AN:

50552

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.490

Heterozygous variant carriers

11495

22990

34484

45979

57474

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

8042

16084

24126

32168

40210

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.249

AC:

37807

AN:

152092

Hom.:

5605

Cov.:

AF XY:

0.253

AC XY:

18845

AN XY:

74344

show subpopulations

African (AFR)

AF:

0.0941

AC:

3909

AN:

41536

American (AMR)

AF:

0.250

AC:

3812

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.269

AC:

934

AN:

3472

East Asian (EAS)

AF:

0.456

AC:

2346

AN:

5148

South Asian (SAS)

AF:

0.232

AC:

1121

AN:

4826

European-Finnish (FIN)

AF:

0.399

AC:

4205

AN:

10550

Middle Eastern (MID)

AF:

0.234

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.305

AC:

20721

AN:

67972

Other (OTH)

AF:

0.253

AC:

536

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1386

2773

4159

5546

6932

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

402

804

1206

1608

2010

<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:

0.284

Hom.:

22140

Bravo

AF:

0.235

Asia WGS

AF:

0.292

AC:

1012

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

2.8

(source)

DANN

Benign

0.28

PhyloP100

1.4

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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