17-73072580-C-A

Position:

• chr17-73072580-C-A

Variant summary

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

The NM_139177.4(SLC39A11):​c.147+12228G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.827 in 151,748 control chromosomes in the GnomAD database, including 51,952 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 0.83 (51950 hom., cov: 28)
  • Exomes 𝑓: 0.83 (2 hom.)
• Consequence: SLC39A11 NM_139177.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.922

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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.877 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC39A11	NM_139177.4	c.147+12228G>T		intron_variant		ENST00000255559.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC39A11	ENST00000255559.8	c.147+12228G>T		intron_variant		1	NM_139177.4	P4

Frequencies

GnomAD3 genomes AF: 0.827 AC: 125354 AN: 151626 Hom.: 51913 Cov.: 28

Gnomad AFR AF: 0.794

Gnomad AMI AF: 0.748

Gnomad AMR AF: 0.838

Gnomad ASJ AF: 0.783

Gnomad EAS AF: 0.899

Gnomad SAS AF: 0.872

Gnomad FIN AF: 0.909

Gnomad MID AF: 0.707

Gnomad NFE AF: 0.827

Gnomad OTH AF: 0.804

GnomAD4 exome AF: 0.833 AC: 5 AN: 6 Hom.: 2 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

Gnomad4 NFE exome AF: 0.833

GnomAD4 genome AF: 0.827 AC: 125442 AN: 151742 Hom.: 51950 Cov.: 28 AF XY: 0.833 AC XY: 61745 AN XY: 74146

Gnomad4 AFR AF: 0.794

Gnomad4 AMR AF: 0.838

Gnomad4 ASJ AF: 0.783

Gnomad4 EAS AF: 0.899

Gnomad4 SAS AF: 0.874

Gnomad4 FIN AF: 0.909

Gnomad4 NFE AF: 0.827

Gnomad4 OTH AF: 0.804

Alfa AF: 0.819 Hom.: 65776

Bravo AF: 0.819

Asia WGS AF: 0.875 AC: 3039 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.16
DANN	Benign	0.57

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: rs8081059; hg19: chr17-71068719;