17-73069260-T-C

Variant names:

• chr17-73069260-T-C
• rs10512594
• NM_139177.4:c.147+15548A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_139177.4(SLC39A11):​c.147+15548A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.846 in 152,196 control chromosomes in the GnomAD database, including 54,606 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 0.85 (54606 hom., cov: 32)
• Consequence: SLC39A11 NM_139177.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0470
• Publications: 3 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.922 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC39A11	NM_139177.4	MANE Select	c.147+15548A>G		intron	N/A	NP_631916.2	Q8N1S5-2
	SLC39A11	NM_001159770.2		c.147+15548A>G		intron	N/A	NP_001153242.1	Q8N1S5-1
	SLC39A11	NM_001352692.2		c.147+15548A>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.147+15548A>G		intron	N/A	ENSP00000255559.3	Q8N1S5-2
	SLC39A11	ENST00000952469.1		c.147+15548A>G		intron	N/A	ENSP00000622528.1
	SLC39A11	ENST00000542342.6	TSL:2	c.147+15548A>G		intron	N/A	ENSP00000445829.2	Q8N1S5-1

Frequencies

GnomAD3 genomes AF: 0.846 AC: 128638 AN: 152078 Hom.: 54554 Cov.: 32

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.747

Gnomad AMR AF: 0.868

Gnomad ASJ AF: 0.811

Gnomad EAS AF: 0.943

Gnomad SAS AF: 0.881

Gnomad FIN AF: 0.930

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.840

Gnomad OTH AF: 0.823

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

GnomAD4 genome AF: 0.846 AC: 128748 AN: 152196 Hom.: 54606 Cov.: 32 AF XY: 0.852 AC XY: 63393 AN XY: 74402

African (AFR) AF: 0.817 AC: 33909 AN: 41506

American (AMR) AF: 0.868 AC: 13260 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.811 AC: 2816 AN: 3472

East Asian (EAS) AF: 0.944 AC: 4890 AN: 5182

South Asian (SAS) AF: 0.883 AC: 4255 AN: 4820

European-Finnish (FIN) AF: 0.930 AC: 9864 AN: 10610

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.840 AC: 57124 AN: 68014

Other (OTH) AF: 0.823 AC: 1736 AN: 2110

Alfa AF: 0.845 Hom.: 28799

Bravo AF: 0.839

Asia WGS AF: 0.901 AC: 3129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.7
DANN	Benign	0.54
PhyloP100		0.047
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: rs10512594; hg19: chr17-71065399;