17-72830265-G-C

Variant names:

• chr17-72830265-G-C
• rs12943829
• NM_139177.4:c.601+19369C>G

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_139177.4(SLC39A11):​c.601+19369C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00595 in 152,018 control chromosomes in the GnomAD database, including 4 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 0.0059 (4 hom., cov: 31)
• Consequence: SLC39A11 NM_139177.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.594
• Publications: 4 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 -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BS2: High Homozygotes in GnomAd4 at 4 AR gene

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC39A11	NM_139177.4	MANE Select	c.601+19369C>G		intron	N/A	NP_631916.2	Q8N1S5-2
	SLC39A11	NM_001159770.2		c.622+19369C>G		intron	N/A	NP_001153242.1	Q8N1S5-1
	SLC39A11	NM_001352692.2		c.622+19369C>G		intron	N/A	NP_001339621.1	Q8N1S5-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC39A11	ENST00000255559.8	TSL:1 MANE Select	c.601+19369C>G		intron	N/A	ENSP00000255559.3	Q8N1S5-2
	SLC39A11	ENST00000952469.1		c.601+19369C>G		intron	N/A	ENSP00000622528.1
	SLC39A11	ENST00000542342.6	TSL:2	c.622+19369C>G		intron	N/A	ENSP00000445829.2	Q8N1S5-1

Frequencies

GnomAD3 genomes AF: 0.00596 AC: 905 AN: 151920 Hom.: 4 Cov.: 31

Gnomad AFR AF: 0.00534

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00374

Gnomad ASJ AF: 0.00893

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00290

Gnomad FIN AF: 0.00314

Gnomad MID AF: 0.0287

Gnomad NFE AF: 0.00771

Gnomad OTH AF: 0.00768

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

GnomAD4 genome AF: 0.00595 AC: 904 AN: 152018 Hom.: 4 Cov.: 31 AF XY: 0.00545 AC XY: 405 AN XY: 74282

African (AFR) AF: 0.00538 AC: 223 AN: 41480

American (AMR) AF: 0.00373 AC: 57 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.00893 AC: 31 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5166

South Asian (SAS) AF: 0.00270 AC: 13 AN: 4808

European-Finnish (FIN) AF: 0.00314 AC: 33 AN: 10522

Middle Eastern (MID) AF: 0.0274 AC: 8 AN: 292

European-Non Finnish (NFE) AF: 0.00769 AC: 523 AN: 67984

Other (OTH) AF: 0.00760 AC: 16 AN: 2104

Alfa AF: 0.00655 Hom.: 3

Bravo AF: 0.00604

Asia WGS AF: 0.00202 AC: 7 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.093
DANN	Benign	0.49
PhyloP100		-0.59
Mutation Taster		=100/0	polymorphism

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: rs12943829; hg19: chr17-70826404;