17-72686473-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_139177.4(SLC39A11):c.672-37205G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 152,142 control chromosomes in the GnomAD database, including 2,688 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 0.15 (2688 hom., cov: 32)
• Consequence: SLC39A11 NM_139177.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.417

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.327 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC39A11	NM_139177.4	c.672-37205G>C		intron_variant		ENST00000255559.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC39A11	ENST00000255559.8	c.672-37205G>C		intron_variant		1	NM_139177.4	P4
SLC39A11	ENST00000542342.6	c.693-37205G>C		intron_variant		2		A1
SLC39A11	ENST00000582769.5	c.420-37205G>C		intron_variant		5
SLC39A11	ENST00000579988.1	n.99-37205G>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22061 AN: 152024 Hom.: 2673 Cov.: 32

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.0361

Gnomad SAS AF: 0.0408

Gnomad FIN AF: 0.0223

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0795

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.145 AC: 22125 AN: 152142 Hom.: 2688 Cov.: 32 AF XY: 0.139 AC XY: 10321 AN XY: 74404

Gnomad4 AFR AF: 0.331

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.100

Gnomad4 EAS AF: 0.0361

Gnomad4 SAS AF: 0.0410

Gnomad4 FIN AF: 0.0223

Gnomad4 NFE AF: 0.0796

Gnomad4 OTH AF: 0.139

Alfa AF: 0.0286 Hom.: 28

Bravo AF: 0.162

Asia WGS AF: 0.0680 AC: 237 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	6.7
Dann	Benign	0.67

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

Publications

LitVar

Other links and lift over

dbSNP: rs8077681; hg19: chr17-70682612;