rs2293576

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001128225.3(SLC39A13):c.573G>A(p.Ala191Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 1,613,866 control chromosomes in the GnomAD database, including 87,445 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.25 ( 5897 hom., cov: 33)

Exomes 𝑓: 0.33 ( 81548 hom. )

Consequence

SLC39A13
NM_001128225.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: 0.557

Publications

57 publications found

Variant links:

Genes affected

SLC39A13 (HGNC:20859): (solute carrier family 39 member 13) This gene encodes a member of the LIV-1 subfamily of the ZIP transporter family. The encoded transmembrane protein functions as a zinc transporter. Mutations in this gene have been associated with the spondylocheiro dysplastic form of Ehlers-Danlos syndrome. Alternate transcript variants have been found for this gene. [provided by RefSeq, Jan 2016]

SLC39A13 Gene-Disease associations (from GenCC):

Ehlers-Danlos syndrome, spondylocheirodysplastic type
Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), PanelApp Australia, Ambry Genetics, G2P, Orphanet, Genomics England PanelApp
spondyloepimetaphyseal dysplasia-abnormal dentition syndrome
Inheritance: AR Classification: DEFINITIVE Submitted by: G2P

SLC39A13 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.73).

BP6

Variant 11-47413435-G-A is Benign according to our data. Variant chr11-47413435-G-A is described in ClinVar as Benign. ClinVar VariationId is 384707.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.557 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC39A13	NM_001128225.3 link	c.573G>A	p.Ala191Ala	synonymous_variant	Exon 5 of 10	ENST00000362021.9	NP_001121697.2	Q96H72-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC39A13	ENST00000362021.9 link	c.573G>A	p.Ala191Ala	synonymous_variant	Exon 5 of 10	1	NM_001128225.3	ENSP00000354689.4		Q96H72-1

Frequencies

GnomAD3 genomes

AF:

0.249

AC:

37789

AN:

152046

Hom.:

5899

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0618

Gnomad AMI

AF:

0.298

Gnomad AMR

AF:

0.230

Gnomad ASJ

AF:

0.347

Gnomad EAS

AF:

0.367

Gnomad SAS

AF:

0.452

Gnomad FIN

AF:

0.262

Gnomad MID

AF:

0.250

Gnomad NFE

AF:

0.334

Gnomad OTH

AF:

0.291

GnomAD2 exomes

AF:

0.310

AC:

77694

AN:

250940

AF XY:

0.325

show subpopulations

Gnomad AFR exome

AF:

0.0597

Gnomad AMR exome

AF:

0.191

Gnomad ASJ exome

AF:

0.345

Gnomad EAS exome

AF:

0.373

Gnomad FIN exome

AF:

0.266

Gnomad NFE exome

AF:

0.335

Gnomad OTH exome

AF:

0.322

GnomAD4 exome

AF:

0.327

AC:

478352

AN:

1461700

Hom.:

81548

Cov.:

AF XY:

0.332

AC XY:

241608

AN XY:

727170

show subpopulations

African (AFR)

AF:

0.0529

AC:

1772

AN:

33476

American (AMR)

AF:

0.197

AC:

8806

AN:

44714

Ashkenazi Jewish (ASJ)

AF:

0.350

AC:

9143

AN:

26126

East Asian (EAS)

AF:

0.308

AC:

12222

AN:

39692

South Asian (SAS)

AF:

0.451

AC:

38874

AN:

86246

European-Finnish (FIN)

AF:

0.270

AC:

14435

AN:

53404

Middle Eastern (MID)

AF:

0.306

AC:

1763

AN:

5764

European-Non Finnish (NFE)

AF:

0.334

AC:

371700

AN:

1111898

Other (OTH)

AF:

0.325

AC:

19637

AN:

60380

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.472

Heterozygous variant carriers

21042

42083

63125

84166

105208

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11894

23788

35682

47576

59470

<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:

37780

AN:

152166

Hom.:

5897

Cov.:

AF XY:

0.248

AC XY:

18424

AN XY:

74376

show subpopulations

African (AFR)

AF:

0.0617

AC:

2561

AN:

41528

American (AMR)

AF:

0.231

AC:

3528

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.347

AC:

1205

AN:

3470

East Asian (EAS)

AF:

0.366

AC:

1892

AN:

5164

South Asian (SAS)

AF:

0.452

AC:

2181

AN:

4826

European-Finnish (FIN)

AF:

0.262

AC:

2776

AN:

10592

Middle Eastern (MID)

AF:

0.248

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.334

AC:

22682

AN:

67966

Other (OTH)

AF:

0.288

AC:

610

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1398

2797

4195

5594

6992

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

406

812

1218

1624

2030

<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:

0.315

Hom.:

15735

Bravo

AF:

0.234

Asia WGS

AF:

0.393

AC:

1367

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Sep 30, 2016

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. -

Apr 25, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Ehlers-Danlos syndrome, spondylocheirodysplastic type

Benign:2

Feb 04, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Jul 15, 2021

Genome-Nilou Lab

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not provided

Benign:1

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

BayesDel_noAF

Benign

-0.73

CADD

Benign

5.4

(source)

DANN

Benign

0.85

PhyloP100

0.56

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

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over