11-47409978-G-A

Position:

• chr11-47409978-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001128225.3(SLC39A13):​c.-8-109G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 1,325,542 control chromosomes in the GnomAD database, including 22,693 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.21 (4110 hom., cov: 34)
  • Exomes 𝑓: 0.16 (18583 hom.)
• Consequence: SLC39A13 NM_001128225.3 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.627

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]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BP6: Variant 11-47409978-G-A is Benign according to our data. Variant chr11-47409978-G-A is described in ClinVar as [Benign]. Clinvar id is 1277095.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC39A13	NM_001128225.3	c.-8-109G>A		intron_variant		ENST00000362021.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC39A13	ENST00000362021.9	c.-8-109G>A		intron_variant		1	NM_001128225.3	P4

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32568 AN: 152138 Hom.: 4113 Cov.: 34

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.302

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.159

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.171

GnomAD4 exome AF: 0.164 AC: 192290 AN: 1173286 Hom.: 18583 Cov.: 16 AF XY: 0.163 AC XY: 96509 AN XY: 593626

Gnomad4 AFR exome AF: 0.316

Gnomad4 AMR exome AF: 0.305

Gnomad4 ASJ exome AF: 0.134

Gnomad4 EAS exome AF: 0.375

Gnomad4 SAS exome AF: 0.170

Gnomad4 FIN exome AF: 0.236

Gnomad4 NFE exome AF: 0.140

Gnomad4 OTH exome AF: 0.158

GnomAD4 genome AF: 0.214 AC: 32571 AN: 152256 Hom.: 4110 Cov.: 34 AF XY: 0.221 AC XY: 16422 AN XY: 74448

Gnomad4 AFR AF: 0.321

Gnomad4 AMR AF: 0.226

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.303

Gnomad4 SAS AF: 0.166

Gnomad4 FIN AF: 0.266

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.169

Alfa AF: 0.150 Hom.: 1125

Bravo AF: 0.217

Asia WGS AF: 0.202 AC: 699 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 26, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	11
DANN	Benign	0.88

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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

Other links and lift over

dbSNP: rs753812; hg19: chr11-47431529; COSMIC: COSV61521726; COSMIC: COSV61521726;