rs2466510

Variant names:

• chr17-72966033-T-A
• rs2466510
• NM_139177.4:c.307-18158A>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 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=-0.97).
• 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 rank	MANE	Protein	UniProt
SLC39A11	NM_139177.4	c.307-18158A>T		intron_variant	Intron 4 of 9	ENST00000255559.8	NP_631916.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC39A11	ENST00000255559.8	c.307-18158A>T		intron_variant	Intron 4 of 9	1	NM_139177.4	ENSP00000255559.3

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

African (AFR) AF: 0.796 AC: 33062 AN: 41532

American (AMR) AF: 0.968 AC: 14814 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.969 AC: 3365 AN: 3472

East Asian (EAS) AF: 0.896 AC: 4638 AN: 5178

South Asian (SAS) AF: 0.958 AC: 4621 AN: 4824

European-Finnish (FIN) AF: 0.908 AC: 9636 AN: 10616

Middle Eastern (MID) AF: 0.976 AC: 287 AN: 294

European-Non Finnish (NFE) AF: 0.985 AC: 66992 AN: 68046

Other (OTH) AF: 0.942 AC: 1993 AN: 2116

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
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2466510; hg19: chr17-70962172;