chr8-117172544-C-T

Variant names:

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_173851.3(SLC30A8):c.973C>T(p.Arg325Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.296 in 1,613,268 control chromosomes in the GnomAD database, including 73,380 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign,risk factor (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R325Q) has been classified as Benign.

Frequency

Genomes: 𝑓 0.25 ( 5580 hom., cov: 33)

Exomes 𝑓: 0.30 ( 67800 hom. )

Consequence

SLC30A8
NM_173851.3 missense

Scores

Clinical Significance

Benign; risk factor no assertion criteria provided B:1O:1

Conservation

PhyloP100: -0.742

Publications

731 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 -13 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=9.0557337E-4).

BP6

Variant 8-117172544-C-T is Benign according to our data. Variant chr8-117172544-C-T is described in ClinVar as Benign|risk_factor. ClinVar VariationId is 1000.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_173851.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
SLC30A8	NM_173851.3	MANE Select	c.973C>T	p.Arg325Trp	missense	Exon 8 of 8	NP_776250.2
SLC30A8	NM_001172811.2		c.826C>T	p.Arg276Trp	missense	Exon 10 of 10	NP_001166282.1
SLC30A8	NM_001172813.2		c.826C>T	p.Arg276Trp	missense	Exon 11 of 11	NP_001166284.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
SLC30A8	ENST00000456015.7	TSL:1 MANE Select	c.973C>T	p.Arg325Trp	missense	Exon 8 of 8	ENSP00000415011.2
SLC30A8	ENST00000519688.5	TSL:1	c.826C>T	p.Arg276Trp	missense	Exon 9 of 9	ENSP00000431069.1
SLC30A8	ENST00000521243.5	TSL:1	c.826C>T	p.Arg276Trp	missense	Exon 10 of 10	ENSP00000428545.1

Frequencies

GnomAD3 genomes

AF:

0.248

AC:

37664

AN:

152022

Hom.:

5578

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0923

Gnomad AMI

AF:

0.168

Gnomad AMR

AF:

0.249

Gnomad ASJ

AF:

0.263

Gnomad EAS

AF:

0.451

Gnomad SAS

AF:

0.232

Gnomad FIN

AF:

0.400

Gnomad MID

AF:

0.231

Gnomad NFE

AF:

0.304

Gnomad OTH

AF:

0.254

GnomAD2 exomes

AF:

0.288

AC:

71769

AN:

249394

AF XY:

0.287

show subpopulations

Gnomad AFR exome

AF:

0.0873

Gnomad AMR exome

AF:

0.257

Gnomad ASJ exome

AF:

0.261

Gnomad EAS exome

AF:

0.439

Gnomad FIN exome

AF:

0.380

Gnomad NFE exome

AF:

0.302

Gnomad OTH exome

AF:

0.286

GnomAD4 exome

AF:

0.301

AC:

439230

AN:

1461128

Hom.:

67800

Cov.:

AF XY:

0.300

AC XY:

217715

AN XY:

726894

show subpopulations

African (AFR)

AF:

0.0809

AC:

2705

AN:

33422

American (AMR)

AF:

0.254

AC:

11357

AN:

44670

Ashkenazi Jewish (ASJ)

AF:

0.262

AC:

6837

AN:

26110

East Asian (EAS)

AF:

0.424

AC:

16813

AN:

39690

South Asian (SAS)

AF:

0.234

AC:

20170

AN:

86248

European-Finnish (FIN)

AF:

0.378

AC:

20184

AN:

53412

Middle Eastern (MID)

AF:

0.205

AC:

1181

AN:

5752

European-Non Finnish (NFE)

AF:

0.308

AC:

342556

AN:

1111484

Other (OTH)

AF:

0.289

AC:

17427

AN:

60340

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.467

Heterozygous variant carriers

17409

34818

52228

69637

87046

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11240

22480

33720

44960

56200

<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:

0.248

AC:

37676

AN:

152140

Hom.:

5580

Cov.:

AF XY:

0.253

AC XY:

18802

AN XY:

74370

show subpopulations

African (AFR)

AF:

0.0922

AC:

3829

AN:

41542

American (AMR)

AF:

0.249

AC:

3812

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.263

AC:

912

AN:

3470

East Asian (EAS)

AF:

0.451

AC:

2314

AN:

5136

South Asian (SAS)

AF:

0.232

AC:

1116

AN:

4812

European-Finnish (FIN)

AF:

0.400

AC:

4240

AN:

10598

Middle Eastern (MID)

AF:

0.235

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.304

AC:

20698

AN:

67984

Other (OTH)

AF:

0.252

AC:

533

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1448

2897

4345

5794

7242

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

400

800

1200

1600

2000

<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.:

29326

Bravo

AF:

0.234

TwinsUK

AF:

0.298

AC:

1104

ALSPAC

AF:

0.299

AC:

1151

ESP6500AA

AF:

0.0967

AC:

426

ESP6500EA

AF:

0.298

AC:

2564

ExAC

AF:

0.285

AC:

34581

Asia WGS

AF:

0.285

AC:

989

AN:

3476

EpiCase

AF:

0.297

EpiControl

AF:

0.287

ClinVar

Significance: Benign; risk factor

Submissions summary: Benign:1Other:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

SLC30A8-related disorder

Benign:1

Oct 21, 2019

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).

Diabetes mellitus type 2, susceptibility to

Other:1

Jun 01, 2007

OMIM

Significance:risk factor

Review Status:no assertion criteria provided

Collection Method:literature only

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.075

BayesDel_addAF

Benign

-0.61

BayesDel_noAF

Benign

-0.50

CADD

Benign

9.8

(source)

DANN

Uncertain

0.98

DEOGEN2

Benign

0.22

Eigen

Benign

-0.69

Eigen_PC

Benign

-0.69

FATHMM_MKL

Benign

0.088

LIST_S2

Benign

0.24

MetaRNN

Benign

0.00091

MetaSVM

Benign

-0.94

MutationAssessor

Benign

1.7

PhyloP100

-0.74

PrimateAI

Benign

0.17

PROVEAN

Benign

-1.9

REVEL

Benign

0.12

Sift

Benign

0.044

Sift4G

Uncertain

0.056

Polyphen

0.0020

Vest4

0.089

MPC

0.048

ClinPred

0.032

GERP RS

-1.8

Varity_R

0.095

gMVP

0.46

Mutation Taster

=99/1

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over