rs2293578

Positions:

• chr11-47415852-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001128225.3(SLC39A13):​c.*489C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 231,064 control chromosomes in the GnomAD database, including 10,046 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.28 (6500 hom., cov: 32)
  • Exomes 𝑓: 0.28 (3546 hom.)
• Consequence: SLC39A13 NM_001128225.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.55

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.364 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC39A13	NM_001128225.3	c.*489C>T		3_prime_UTR_variant	10/10	ENST00000362021.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC39A13	ENST00000362021.9	c.*489C>T		3_prime_UTR_variant	10/10	1	NM_001128225.3	P4
SLC39A13	ENST00000354884.8	c.*489C>T		3_prime_UTR_variant	10/10	1		A1
SLC39A13	ENST00000524928.1	c.*1935C>T		3_prime_UTR_variant	5/5	2
SLC39A13	ENST00000533076.5	c.*246+356C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43155 AN: 152008 Hom.: 6486 Cov.: 32

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.307

GnomAD4 exome AF: 0.283 AC: 22303 AN: 78938 Hom.: 3546 Cov.: 0 AF XY: 0.283 AC XY: 11976 AN XY: 42324

Gnomad4 AFR exome AF: 0.139

Gnomad4 AMR exome AF: 0.364

Gnomad4 ASJ exome AF: 0.273

Gnomad4 EAS exome AF: 0.262

Gnomad4 SAS exome AF: 0.245

Gnomad4 FIN exome AF: 0.279

Gnomad4 NFE exome AF: 0.295

Gnomad4 OTH exome AF: 0.295

GnomAD4 genome AF: 0.284 AC: 43191 AN: 152126 Hom.: 6500 Cov.: 32 AF XY: 0.285 AC XY: 21204 AN XY: 74368

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.372

Gnomad4 ASJ AF: 0.289

Gnomad4 EAS AF: 0.291

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.303

Gnomad4 NFE AF: 0.324

Gnomad4 OTH AF: 0.314

Alfa AF: 0.308 Hom.: 1696

Bravo AF: 0.285

Asia WGS AF: 0.298 AC: 1038 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	11
DANN	Benign	0.68
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.1

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

Publications

LitVar

Other links and lift over

dbSNP: rs2293578; hg19: chr11-47437403; COSMIC: COSV54080149; COSMIC: COSV54080149;