rs2466510

Positions:

• chr17-72966033-T-A
• chr17-72966033-T-G

Variant summary

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

The NM_139177.4(SLC39A11):​c.307-18158A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.921 in 152,290 control chromosomes in the GnomAD database, including 65,146 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 0.92 (65146 hom., cov: 33)
• Consequence: SLC39A11 NM_139177.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40

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=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.978 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC39A11	NM_139177.4	c.307-18158A>T		intron_variant		ENST00000255559.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC39A11	ENST00000255559.8	c.307-18158A>T		intron_variant		1	NM_139177.4	P4

Frequencies

GnomAD3 genomes AF: 0.922 AC: 140254 AN: 152172 Hom.: 65127 Cov.: 33

Gnomad AFR AF: 0.797

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.968

Gnomad ASJ AF: 0.969

Gnomad EAS AF: 0.896

Gnomad SAS AF: 0.958

Gnomad FIN AF: 0.908

Gnomad MID AF: 0.978

Gnomad NFE AF: 0.985

Gnomad OTH AF: 0.942

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

GnomAD4 genome AF: 0.921 AC: 140320 AN: 152290 Hom.: 65146 Cov.: 33 AF XY: 0.918 AC XY: 68360 AN XY: 74460

Gnomad4 AFR AF: 0.796

Gnomad4 AMR AF: 0.968

Gnomad4 ASJ AF: 0.969

Gnomad4 EAS AF: 0.896

Gnomad4 SAS AF: 0.958

Gnomad4 FIN AF: 0.908

Gnomad4 NFE AF: 0.985

Gnomad4 OTH AF: 0.942

Alfa AF: 0.949 Hom.: 3290

Bravo AF: 0.921

Asia WGS AF: 0.905 AC: 3149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.27
DANN	Benign	0.47

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs2466510; hg19: chr17-70962172;