11-47408641-TCGCCGC-TCGCCGCCGC

Variant names:

• chr11-47408641-T-TCGC
• rs551004316
• NM_001128225.3:c.-14_-12dupCGC

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001128225.3(SLC39A13):​c.-14_-12dupCGC variant causes a splice region 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 splice_region
• Clinical Significance: Benign criteria provided, single submitter B:2
• Conservation: PhyloP100: 0.167
• Publications: 1 publications found

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]

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]

SLC39A13-AS1 (HGNC:56351): (SLC39A13 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001128225.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC39A13	NM_001128225.3	MANE Select	c.-14_-12dupCGC		splice_region	Exon 1 of 10	NP_001121697.2	Q96H72-1
	SLC39A13	NM_001128225.3	MANE Select	c.-14_-12dupCGC		5_prime_UTR	Exon 1 of 10	NP_001121697.2	Q96H72-1
	SLC39A13	NM_001441271.1		c.-93_-91dupCGC		splice_region	Exon 1 of 11	NP_001428200.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC39A13	ENST00000362021.9	TSL:1 MANE Select	c.-14_-12dupCGC		splice_region	Exon 1 of 10	ENSP00000354689.4	Q96H72-1
	SLC39A13	ENST00000354884.8	TSL:1	c.-35_-33dupCGC		splice_region	Exon 1 of 10	ENSP00000346956.4	Q96H72-2
	SLC39A13	ENST00000362021.9	TSL:1 MANE Select	c.-14_-12dupCGC		5_prime_UTR	Exon 1 of 10	ENSP00000354689.4	Q96H72-1

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

African (AFR) AF: 0.00 AC: 0 AN: 6

American (AMR) AF: 0.583 AC: 7 AN: 12

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 4 AN: 10

East Asian (EAS) AF: 0.463 AC: 25 AN: 54

South Asian (SAS) AF: 0.353 AC: 233 AN: 660

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.467 AC: 268 AN: 574

Other (OTH) AF: 0.500 AC: 11 AN: 22

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

African (AFR) AF: 0.222 AC: 9109 AN: 40986

American (AMR) AF: 0.376 AC: 5637 AN: 15000

Ashkenazi Jewish (ASJ) AF: 0.291 AC: 999 AN: 3432

East Asian (EAS) AF: 0.289 AC: 1447 AN: 5006

South Asian (SAS) AF: 0.300 AC: 1438 AN: 4798

European-Finnish (FIN) AF: 0.310 AC: 2937 AN: 9478

Middle Eastern (MID) AF: 0.391 AC: 111 AN: 284

European-Non Finnish (NFE) AF: 0.327 AC: 21851 AN: 66760

Other (OTH) AF: 0.324 AC: 669 AN: 2062

Alfa AF: 0.156 Hom.: 293

Asia WGS AF: 0.274 AC: 937 AN: 3414

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.17
Mutation Taster		=99/1	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs551004316; hg19: chr11-47430192; COSMIC: COSV61522700; COSMIC: COSV61522700;