rs9944433

Positions:

• chr17-73085813-G-A

Variant summary

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

The NM_139177.4(SLC39A11):​c.109-967C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 151,818 control chromosomes in the GnomAD database, including 7,419 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 0.30 (7419 hom., cov: 31)
• Consequence: SLC39A11 NM_139177.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.29

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC39A11	NM_139177.4	c.109-967C>T		intron_variant		ENST00000255559.8	NP_631916.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC39A11	ENST00000255559.8	c.109-967C>T		intron_variant		1	NM_139177.4	ENSP00000255559	P4

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46076 AN: 151700 Hom.: 7413 Cov.: 31

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.353

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.304 AC: 46089 AN: 151818 Hom.: 7419 Cov.: 31 AF XY: 0.297 AC XY: 22016 AN XY: 74196

Gnomad4 AFR AF: 0.233

Gnomad4 AMR AF: 0.355

Gnomad4 ASJ AF: 0.501

Gnomad4 EAS AF: 0.198

Gnomad4 SAS AF: 0.206

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.348

Gnomad4 OTH AF: 0.350

Alfa AF: 0.330 Hom.: 4139

Bravo AF: 0.317

Asia WGS AF: 0.214 AC: 751 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.0
DANN	Benign	0.54

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: rs9944433; hg19: chr17-71081952;