rs1126965

Positions:

• chr17-72646651-C-G

Variant summary

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

The NM_139177.4(SLC39A11):​c.*933G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 152,546 control chromosomes in the GnomAD database, including 4,775 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 0.25 (4772 hom., cov: 33)
  • Exomes 𝑓: 0.17 (3 hom.)
• Consequence: SLC39A11 NM_139177.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.376

Genes affected

SLC39A11 (HGNC:14463): (solute carrier family 39 member 11) Predicted to enable zinc ion transmembrane transporter activity. Predicted to be involved in zinc ion transmembrane transport. Predicted to be located in Golgi apparatus; nucleus; and plasma membrane. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC39A11	NM_139177.4	c.*933G>C		3_prime_UTR_variant	10/10	ENST00000255559.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC39A11	ENST00000255559.8	c.*933G>C		3_prime_UTR_variant	10/10	1	NM_139177.4	P4
SLC39A11	ENST00000542342.6	c.*933G>C		3_prime_UTR_variant	10/10	2		A1

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37756 AN: 151996 Hom.: 4763 Cov.: 33

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.263

GnomAD4 exome AF: 0.174 AC: 75 AN: 432 Hom.: 3 Cov.: 0 AF XY: 0.177 AC XY: 46 AN XY: 260

Gnomad4 FIN exome AF: 0.174

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.248 AC: 37798 AN: 152114 Hom.: 4772 Cov.: 33 AF XY: 0.243 AC XY: 18052 AN XY: 74380

Gnomad4 AFR AF: 0.260

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.246

Gnomad4 EAS AF: 0.116

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.188

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.264

Alfa AF: 0.248 Hom.: 689

Bravo AF: 0.257

Asia WGS AF: 0.192 AC: 672 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.76

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: rs1126965; hg19: chr17-70642790;