rs2293576

Positions:

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001128225.3(SLC39A13):c.573G>A(p.Ala191=) 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:4

Conservation

PhyloP100: 0.557

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 id is 384707.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-47413435-G-A is described in Lovd as [Benign].

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/exons	MANE	UniProt
SLC39A13	NM_001128225.3 linkuse as main transcript	c.573G>A	p.Ala191=	synonymous_variant	5/10	ENST00000362021.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC39A13	ENST00000362021.9 linkuse as main transcript	c.573G>A	p.Ala191=	synonymous_variant	5/10	1	NM_001128225.3	P4	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

GnomAD3 exomes

AF:

0.310

AC:

77694

AN:

250940

Hom.:

13532

AF XY:

0.325

AC XY:

44106

AN XY:

135754

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 SAS exome

AF:

0.460

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

Gnomad4 AFR exome

AF:

0.0529

Gnomad4 AMR exome

AF:

0.197

Gnomad4 ASJ exome

AF:

0.350

Gnomad4 EAS exome

AF:

0.308

Gnomad4 SAS exome

AF:

0.451

Gnomad4 FIN exome

AF:

0.270

Gnomad4 NFE exome

AF:

0.334

Gnomad4 OTH exome

AF:

0.325

GnomAD4 genome

AF:

0.248

AC:

37780

AN:

152166

Hom.:

5897

Cov.:

AF XY:

0.248

AC XY:

18424

AN XY:

74376

show subpopulations

Gnomad4 AFR

AF:

0.0617

Gnomad4 AMR

AF:

0.231

Gnomad4 ASJ

AF:

0.347

Gnomad4 EAS

AF:

0.366

Gnomad4 SAS

AF:

0.452

Gnomad4 FIN

AF:

0.262

Gnomad4 NFE

AF:

0.334

Gnomad4 OTH

AF:

0.288

Alfa

AF:

0.317

Hom.:

13253

Bravo

AF:

0.234

Asia WGS

AF:

0.393

AC:

1367

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Benign, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Apr 25, 2016	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 -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Sep 30, 2016	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. -

Ehlers-Danlos syndrome, spondylocheirodysplastic type

Benign:2

Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jul 15, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Invitae	Feb 01, 2024	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

5.4

DANN

Benign

0.85

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over