rs3740030

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_213606.4(SLC16A12):c.49T>G(p.Trp17Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0841 in 1,613,154 control chromosomes in the GnomAD database, including 6,627 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.067 ( 491 hom., cov: 32)

Exomes 𝑓: 0.086 ( 6136 hom. )

Consequence

SLC16A12
NM_213606.4 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 1.31

Publications

18 publications found

Variant links:

Genes affected

SLC16A12 (HGNC:23094): (solute carrier family 16 member 12) This gene encodes a transmembrane transporter that likely plays a role in monocarboxylic acid transport. A mutation in this gene has been associated with juvenile cataracts with microcornea and renal glucosuria. [provided by RefSeq, Mar 2010]

SLC16A12 links:

SLC16A12-AS1 (HGNC:51205): (SLC16A12 antisense RNA 1)

SLC16A12-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0035749376).

BP6

Variant 10-89462530-A-C is Benign according to our data. Variant chr10-89462530-A-C is described in ClinVar as Benign. ClinVar VariationId is 681342.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC16A12	NM_213606.4 link	c.49T>G	p.Trp17Gly	missense_variant	Exon 3 of 8	ENST00000371790.5	NP_998771.3	Q6ZSM3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC16A12	ENST00000371790.5 link	c.49T>G	p.Trp17Gly	missense_variant	Exon 3 of 8	2	NM_213606.4	ENSP00000360855.4		Q6ZSM3

Frequencies

GnomAD3 genomes

AF:

0.0674

AC:

10247

AN:

152030

Hom.:

493

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0161

Gnomad AMI

AF:

0.0307

Gnomad AMR

AF:

0.0426

Gnomad ASJ

AF:

0.0573

Gnomad EAS

AF:

0.209

Gnomad SAS

AF:

0.0242

Gnomad FIN

AF:

0.119

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0899

Gnomad OTH

AF:

0.0637

GnomAD2 exomes

AF:

0.0796

AC:

19814

AN:

249050

AF XY:

0.0786

show subpopulations

Gnomad AFR exome

AF:

0.0152

Gnomad AMR exome

AF:

0.0306

Gnomad ASJ exome

AF:

0.0619

Gnomad EAS exome

AF:

0.212

Gnomad FIN exome

AF:

0.113

Gnomad NFE exome

AF:

0.0929

Gnomad OTH exome

AF:

0.0738

GnomAD4 exome

AF:

0.0859

AC:

125507

AN:

1461004

Hom.:

6136

Cov.:

AF XY:

0.0843

AC XY:

61251

AN XY:

726826

show subpopulations

African (AFR)

AF:

0.0122

AC:

407

AN:

33458

American (AMR)

AF:

0.0320

AC:

1429

AN:

44674

Ashkenazi Jewish (ASJ)

AF:

0.0614

AC:

1605

AN:

26134

East Asian (EAS)

AF:

0.190

AC:

7530

AN:

39646

South Asian (SAS)

AF:

0.0265

AC:

2281

AN:

86238

European-Finnish (FIN)

AF:

0.112

AC:

5935

AN:

52962

Middle Eastern (MID)

AF:

0.0187

AC:

108

AN:

5766

European-Non Finnish (NFE)

AF:

0.0910

AC:

101194

AN:

1111778

Other (OTH)

AF:

0.0832

AC:

5018

AN:

60348

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.467

Heterozygous variant carriers

6589

13178

19767

26356

32945

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3702

7404

11106

14808

18510

<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:

0.0673

AC:

10238

AN:

152150

Hom.:

491

Cov.:

AF XY:

0.0679

AC XY:

5049

AN XY:

74366

show subpopulations

African (AFR)

AF:

0.0161

AC:

667

AN:

41530

American (AMR)

AF:

0.0425

AC:

649

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.0573

AC:

199

AN:

3470

East Asian (EAS)

AF:

0.208

AC:

1070

AN:

5156

South Asian (SAS)

AF:

0.0243

AC:

117

AN:

4824

European-Finnish (FIN)

AF:

0.119

AC:

1263

AN:

10598

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0899

AC:

6113

AN:

67980

Other (OTH)

AF:

0.0626

AC:

132

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

478

957

1435

1914

2392

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

124

248

372

496

620

<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:

0.0801

Hom.:

1906

Bravo

AF:

0.0608

TwinsUK

AF:

0.0928

AC:

344

ALSPAC

AF:

0.0944

AC:

364

ESP6500AA

AF:

0.0220

AC:

ESP6500EA

AF:

0.0850

AC:

731

ExAC

AF:

0.0794

AC:

9635

Asia WGS

AF:

0.100

AC:

347

AN:

3478

EpiCase

AF:

0.0809

EpiControl

AF:

0.0808

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Jan 23, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Mar 24, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.052

BayesDel_addAF

Benign

-0.74

BayesDel_noAF

Benign

-0.69

CADD

Benign

(source)

DANN

Benign

0.76

DEOGEN2

Benign

0.23

T;.

Eigen

Benign

-0.61

Eigen_PC

Benign

-0.59

FATHMM_MKL

Benign

0.043

LIST_S2

Benign

0.24

T;T

MetaRNN

Benign

0.0036

T;T

MetaSVM

Benign

-0.93

PhyloP100

1.3

PrimateAI

Benign

0.27

PROVEAN

Benign

0.040

N;D

REVEL

Benign

0.040

Sift

Benign

0.46

T;.

Vest4

0.033

MPC

0.28

ClinPred

0.0023

GERP RS

0.62

Varity_R

0.40

gMVP

0.47

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over