rs4969049

Variant names:

• chr17-73004801-T-C
• rs4969049
• NM_139177.4:c.306+26755A>G

Your query was ambiguous. Multiple possible variants found:

• chr17-73004801-T-C
• chr17-73004801-T-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+26755A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 152,176 control chromosomes in the GnomAD database, including 2,246 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 0.17 (2246 hom., cov: 33)
• Consequence: SLC39A11 NM_139177.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.36
• Publications: 6 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.232 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.306+26755A>G		intron	N/A	NP_631916.2	Q8N1S5-2
	SLC39A11	NM_001159770.2		c.306+26755A>G		intron	N/A	NP_001153242.1	Q8N1S5-1
	SLC39A11	NM_001352692.2		c.306+26755A>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.306+26755A>G		intron	N/A	ENSP00000255559.3	Q8N1S5-2
	SLC39A11	ENST00000952469.1		c.306+26755A>G		intron	N/A	ENSP00000622528.1
	SLC39A11	ENST00000542342.6	TSL:2	c.306+26755A>G		intron	N/A	ENSP00000445829.2	Q8N1S5-1

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25360 AN: 152058 Hom.: 2243 Cov.: 33

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.167 AC: 25394 AN: 152176 Hom.: 2246 Cov.: 33 AF XY: 0.166 AC XY: 12346 AN XY: 74428

African (AFR) AF: 0.236 AC: 9798 AN: 41504

American (AMR) AF: 0.174 AC: 2658 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 456 AN: 3466

East Asian (EAS) AF: 0.206 AC: 1065 AN: 5166

South Asian (SAS) AF: 0.106 AC: 514 AN: 4830

European-Finnish (FIN) AF: 0.118 AC: 1247 AN: 10600

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9152 AN: 68010

Other (OTH) AF: 0.171 AC: 361 AN: 2108

Alfa AF: 0.151 Hom.: 4950

Bravo AF: 0.175

Asia WGS AF: 0.158 AC: 550 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.4
DANN	Benign	0.42
PhyloP100		1.4
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: rs4969049; hg19: chr17-71000940;