NM_139177.4:c.109-967C>T

Variant names:

• chr17-73085813-G-A
• rs9944433
• NM_139177.4:c.109-967C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_139177.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC39A11	NM_139177.4	MANE Select	c.109-967C>T		intron	N/A	NP_631916.2
	SLC39A11	NM_001159770.2		c.109-967C>T		intron	N/A	NP_001153242.1
	SLC39A11	NM_001352692.2		c.109-967C>T		intron	N/A	NP_001339621.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC39A11	ENST00000255559.8	TSL:1 MANE Select	c.109-967C>T		intron	N/A	ENSP00000255559.3
	SLC39A11	ENST00000542342.6	TSL:2	c.109-967C>T		intron	N/A	ENSP00000445829.2
	SLC39A11	ENST00000579732.5	TSL:2	c.109-967C>T		intron	N/A	ENSP00000464525.1

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

African (AFR) AF: 0.233 AC: 9649 AN: 41382

American (AMR) AF: 0.355 AC: 5404 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.501 AC: 1737 AN: 3466

East Asian (EAS) AF: 0.198 AC: 1022 AN: 5174

South Asian (SAS) AF: 0.206 AC: 992 AN: 4814

European-Finnish (FIN) AF: 0.234 AC: 2465 AN: 10526

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.348 AC: 23613 AN: 67926

Other (OTH) AF: 0.350 AC: 736 AN: 2100

Alfa AF: 0.330 Hom.: 5987

Bravo AF: 0.317

Asia WGS AF: 0.214 AC: 751 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.0
DANN	Benign	0.54
PhyloP100		-2.3
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: rs9944433; hg19: chr17-71081952;