rs1126965

Variant names:

• chr17-72646651-C-G
• rs1126965
• NM_139177.4:c.*933G>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SLC39A11	NM_139177.4	c.*933G>C		3_prime_UTR_variant	Exon 10 of 10	ENST00000255559.8	NP_631916.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC39A11	ENST00000255559.8	c.*933G>C		3_prime_UTR_variant	Exon 10 of 10	1	NM_139177.4	ENSP00000255559.3
SLC39A11	ENST00000542342.6	c.*933G>C		3_prime_UTR_variant	Exon 10 of 10	2		ENSP00000445829.2

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.174 AC: 74 AN: 426

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AF: 0.250 AC: 1 AN: 4

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

African (AFR) AF: 0.260 AC: 10765 AN: 41460

American (AMR) AF: 0.277 AC: 4236 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 853 AN: 3472

East Asian (EAS) AF: 0.116 AC: 602 AN: 5176

South Asian (SAS) AF: 0.219 AC: 1059 AN: 4826

European-Finnish (FIN) AF: 0.188 AC: 1990 AN: 10586

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17304 AN: 67994

Other (OTH) AF: 0.264 AC: 558 AN: 2116

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
PhyloP100		0.38
Mutation Taster		=100/0	polymorphism (auto)

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: rs1126965; hg19: chr17-70642790;