11-47408641-T-TCGC

Position:

• chr11-47408641-T-TCGC

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001128225.3(SLC39A13):​c.-14_-12dup variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.30 (6896 hom., cov: 0)
  • Exomes 𝑓: 0.41 (110 hom.)
• Consequence: SLC39A13 NM_001128225.3 5_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:2
• Conservation: PhyloP100: 0.167

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:56351): (SLC39A13 antisense RNA 1)

SPI1 (HGNC:11241): (Spi-1 proto-oncogene) This gene encodes an ETS-domain transcription factor that activates gene expression during myeloid and B-lymphoid cell development. The nuclear protein binds to a purine-rich sequence known as the PU-box found near the promoters of target genes, and regulates their expression in coordination with other transcription factors and cofactors. The protein can also regulate alternative splicing of target genes. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 11-47408641-T-TCGC is Benign according to our data. Variant chr11-47408641-T-TCGC is described in ClinVar as [Benign]. Clinvar id is 517012.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC39A13	NM_001128225.3	c.-14_-12dup		5_prime_UTR_variant	1/10	ENST00000362021.9
SLC39A13-AS1	NR_182305.1	n.331+310_331+311insGCG		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC39A13	ENST00000362021.9	c.-14_-12dup		5_prime_UTR_variant	1/10	1	NM_001128225.3	P4
SLC39A13-AS1	ENST00000666926.1	n.320+310_320+311insGCG		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.300 AC: 44648 AN: 148598 Hom.: 6881 Cov.: 0

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.317

GnomAD4 exome AF: 0.410 AC: 548 AN: 1338 Hom.: 110 Cov.: 0 AF XY: 0.416 AC XY: 349 AN XY: 838

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.583

Gnomad4 ASJ exome AF: 0.400

Gnomad4 EAS exome AF: 0.463

Gnomad4 SAS exome AF: 0.353

Gnomad4 NFE exome AF: 0.467

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.301 AC: 44687 AN: 148700 Hom.: 6896 Cov.: 0 AF XY: 0.301 AC XY: 21852 AN XY: 72498

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.376

Gnomad4 ASJ AF: 0.291

Gnomad4 EAS AF: 0.289

Gnomad4 SAS AF: 0.300

Gnomad4 FIN AF: 0.310

Gnomad4 NFE AF: 0.327

Gnomad4 OTH AF: 0.324

Asia WGS AF: 0.274 AC: 937 AN: 3414

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:2

Benign, flagged submission	clinical testing	GeneDx	Sep 30, 2016	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 30, 2018	- -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs551004316; hg19: chr11-47430192;