rs4969054

Variant names:

• chr17-73016334-G-C
• rs4969054
• NM_139177.4:c.306+15222C>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.306+15222C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.742 in 142,932 control chromosomes in the GnomAD database, including 41,380 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 0.74 (41380 hom., cov: 29)
• Consequence: SLC39A11 NM_139177.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0910
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.872 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC39A11	NM_139177.4	c.306+15222C>G		intron_variant	Intron 4 of 9	ENST00000255559.8	NP_631916.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC39A11	ENST00000255559.8	c.306+15222C>G		intron_variant	Intron 4 of 9	1	NM_139177.4	ENSP00000255559.3

Frequencies

GnomAD3 genomes AF: 0.742 AC: 105987 AN: 142832 Hom.: 41373 Cov.: 29

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.925

Gnomad AMR AF: 0.801

Gnomad ASJ AF: 0.860

Gnomad EAS AF: 0.794

Gnomad SAS AF: 0.858

Gnomad FIN AF: 0.786

Gnomad MID AF: 0.857

Gnomad NFE AF: 0.878

Gnomad OTH AF: 0.766

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

GnomAD4 genome AF: 0.742 AC: 106013 AN: 142932 Hom.: 41380 Cov.: 29 AF XY: 0.742 AC XY: 51751 AN XY: 69760

African (AFR) AF: 0.391 AC: 13333 AN: 34142

American (AMR) AF: 0.802 AC: 11914 AN: 14864

Ashkenazi Jewish (ASJ) AF: 0.860 AC: 2969 AN: 3454

East Asian (EAS) AF: 0.793 AC: 4008 AN: 5052

South Asian (SAS) AF: 0.859 AC: 4096 AN: 4768

European-Finnish (FIN) AF: 0.786 AC: 7861 AN: 10002

Middle Eastern (MID) AF: 0.856 AC: 250 AN: 292

European-Non Finnish (NFE) AF: 0.878 AC: 59201 AN: 67440

Other (OTH) AF: 0.766 AC: 1539 AN: 2008

Alfa AF: 0.765 Hom.: 5896

Bravo AF: 0.682

Asia WGS AF: 0.772 AC: 2656 AN: 3444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.7
DANN	Benign	0.67
PhyloP100		0.091
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: rs4969054; hg19: chr17-71012473;