11-47408907-T-C

Position:

• chr11-47408907-T-C

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.-9+245T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.647 in 152,486 control chromosomes in the GnomAD database, including 31,916 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.65 (31796 hom., cov: 31)
  • Exomes 𝑓: 0.65 (120 hom.)
• Consequence: SLC39A13 NM_001128225.3 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -1.05

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-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BP6: Variant 11-47408907-T-C is Benign according to our data. Variant chr11-47408907-T-C is described in ClinVar as [Benign]. Clinvar id is 1239745.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC39A13	NM_001128225.3	c.-9+245T>C		intron_variant		ENST00000362021.9	NP_001121697.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC39A13	ENST00000362021.9	c.-9+245T>C		intron_variant		1	NM_001128225.3	ENSP00000354689.4

Frequencies

GnomAD3 genomes AF: 0.647 AC: 98181 AN: 151794 Hom.: 31793 Cov.: 31

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.449

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.695

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.695

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.641

GnomAD4 exome AF: 0.653 AC: 375 AN: 574 Hom.: 120 Cov.: 0 AF XY: 0.653 AC XY: 282 AN XY: 432

Gnomad4 AFR exome AF: 0.600

Gnomad4 AMR exome AF: 0.667

Gnomad4 EAS exome AF: 0.750

Gnomad4 SAS exome AF: 0.625

Gnomad4 FIN exome AF: 0.683

Gnomad4 NFE exome AF: 0.653

Gnomad4 OTH exome AF: 0.636

GnomAD4 genome AF: 0.646 AC: 98208 AN: 151912 Hom.: 31796 Cov.: 31 AF XY: 0.647 AC XY: 48047 AN XY: 74242

Gnomad4 AFR AF: 0.607

Gnomad4 AMR AF: 0.606

Gnomad4 ASJ AF: 0.695

Gnomad4 EAS AF: 0.706

Gnomad4 SAS AF: 0.696

Gnomad4 FIN AF: 0.680

Gnomad4 NFE AF: 0.667

Gnomad4 OTH AF: 0.634

Alfa AF: 0.651 Hom.: 8851

Bravo AF: 0.639

Asia WGS AF: 0.681 AC: 2366 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 23, 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	-0.89
CADD	Benign	4.1
DANN	Benign	0.51

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs7937331; hg19: chr11-47430458;