rs2567519

chr17-72792267-G-A

Variant summary

Our verdict is Benign. Variant got -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

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=-0.91).
• 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/exons	MANE	UniProt
SLC39A11	NM_139177.4	c.602-55548C>T		intron_variant		ENST00000255559.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC39A11	ENST00000255559.8	c.602-55548C>T		intron_variant		1	NM_139177.4	P4

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

Gnomad4 AFR AF: 0.440

Gnomad4 AMR AF: 0.524

Gnomad4 ASJ AF: 0.667

Gnomad4 EAS AF: 0.288

Gnomad4 SAS AF: 0.515

Gnomad4 FIN AF: 0.677

Gnomad4 NFE AF: 0.695

Gnomad4 OTH AF: 0.587

Alfa AF: 0.620 Hom.: 5052

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

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: rs2567519; hg19: chr17-70788406;