17-72792267-G-A

Variant names:

• chr17-72792267-G-A
• rs2567519
• NM_139177.4:c.602-55548C>T

Variant summary

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

The NM_139177.4(SLC39A11):​c.602-55548C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.585 in 152,058 control chromosomes in the GnomAD database, including 27,261 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 0.58 (27261 hom., cov: 32)
• Consequence: SLC39A11 NM_139177.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.289
• 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC39A11	NM_139177.4	c.602-55548C>T		intron_variant	Intron 6 of 9	ENST00000255559.8	NP_631916.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC39A11	ENST00000255559.8	c.602-55548C>T		intron_variant	Intron 6 of 9	1	NM_139177.4	ENSP00000255559.3

Frequencies

GnomAD3 genomes AF: 0.585 AC: 88898 AN: 151940 Hom.: 27249 Cov.: 32

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.642

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.667

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.677

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.695

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.585 AC: 88940 AN: 152058 Hom.: 27261 Cov.: 32 AF XY: 0.579 AC XY: 43019 AN XY: 74328

African (AFR) AF: 0.440 AC: 18243 AN: 41470

American (AMR) AF: 0.524 AC: 8007 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.667 AC: 2313 AN: 3468

East Asian (EAS) AF: 0.288 AC: 1484 AN: 5154

South Asian (SAS) AF: 0.515 AC: 2487 AN: 4830

European-Finnish (FIN) AF: 0.677 AC: 7159 AN: 10580

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.695 AC: 47231 AN: 67970

Other (OTH) AF: 0.587 AC: 1238 AN: 2110

Alfa AF: 0.609 Hom.: 9907

Bravo AF: 0.566

Asia WGS AF: 0.410 AC: 1427 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.67
PhyloP100		-0.29
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: rs2567519; hg19: chr17-70788406;