NM_001128225.3:c.-33G>C

Variant names:

• chr11-47408638-G-C
• rs538845170
• NM_001128225.3:c.-33G>C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Moderate BP6_Moderate

The NM_001128225.3(SLC39A13):​c.-33G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00118 in 137,662 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: 𝑓 0.0012 (1 hom., cov: 33)
• Consequence: SLC39A13 NM_001128225.3 5_prime_UTR
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.398
• Publications: 0 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: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.29).
• BP6: Variant 11-47408638-G-C is Benign according to our data. Variant chr11-47408638-G-C is described in ClinVar as Likely_benign. ClinVar VariationId is 512793.Status of the report is criteria_provided_single_submitter, 1 stars.

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.-33G>C		5_prime_UTR	Exon 1 of 10	NP_001121697.2	Q96H72-1
	SLC39A13	NM_001441271.1		c.-112G>C		5_prime_UTR	Exon 1 of 11	NP_001428200.1
	SLC39A13	NM_152264.5		c.-54G>C		5_prime_UTR	Exon 1 of 10	NP_689477.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC39A13	ENST00000362021.9	TSL:1 MANE Select	c.-33G>C		5_prime_UTR	Exon 1 of 10	ENSP00000354689.4	Q96H72-1
	SLC39A13	ENST00000354884.8	TSL:1	c.-54G>C		5_prime_UTR	Exon 1 of 10	ENSP00000346956.4	Q96H72-2
	SLC39A13	ENST00000968896.1		c.-33G>C		5_prime_UTR	Exon 1 of 11	ENSP00000638955.1

Frequencies

GnomAD3 genomes AF: 0.00119 AC: 164 AN: 137578 Hom.: 1 Cov.: 33

Gnomad AFR AF: 0.00384

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000831

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000228

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00106

GnomAD4 exome Cov.: 0

GnomAD4 genome AF: 0.00118 AC: 163 AN: 137662 Hom.: 1 Cov.: 33 AF XY: 0.00115 AC XY: 77 AN XY: 67010

African (AFR) AF: 0.00380 AC: 149 AN: 39220

American (AMR) AF: 0.000830 AC: 11 AN: 13252

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3262

East Asian (EAS) AF: 0.00 AC: 0 AN: 4706

South Asian (SAS) AF: 0.000228 AC: 1 AN: 4392

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8414

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 250

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 61608

Other (OTH) AF: 0.00106 AC: 2 AN: 1890

Alfa AF: 0.0000712 Hom.: 0

Bravo AF: 0.00117

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.29
CADD	Benign	17
DANN	Benign	0.93
PhyloP100		0.40
PromoterAI		-0.15	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
Mutation Taster		=300/0	polymorphism

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

Other links and lift over

dbSNP: rs538845170; hg19: chr11-47430189;