17-72719518-T-C

Variant names:

• chr17-72719518-T-C
• rs2567506
• NM_139177.4:c.671+17132A>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.671+17132A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 152,066 control chromosomes in the GnomAD database, including 25,250 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 0.57 (25250 hom., cov: 33)
• Consequence: SLC39A11 NM_139177.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC39A11	NM_139177.4	c.671+17132A>G		intron_variant	Intron 7 of 9	ENST00000255559.8	NP_631916.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC39A11	ENST00000255559.8	c.671+17132A>G		intron_variant	Intron 7 of 9	1	NM_139177.4	ENSP00000255559.3

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86478 AN: 151948 Hom.: 25216 Cov.: 33

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.643

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.579

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.569 AC: 86574 AN: 152066 Hom.: 25250 Cov.: 33 AF XY: 0.564 AC XY: 41898 AN XY: 74324

African (AFR) AF: 0.611 AC: 25323 AN: 41468

American (AMR) AF: 0.628 AC: 9605 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.643 AC: 2230 AN: 3470

East Asian (EAS) AF: 0.143 AC: 740 AN: 5170

South Asian (SAS) AF: 0.466 AC: 2243 AN: 4816

European-Finnish (FIN) AF: 0.500 AC: 5287 AN: 10578

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.579 AC: 39349 AN: 67962

Other (OTH) AF: 0.566 AC: 1195 AN: 2110

Alfa AF: 0.571 Hom.: 73773

Bravo AF: 0.579

Asia WGS AF: 0.335 AC: 1169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.098
DANN	Benign	0.41
PhyloP100		-2.0
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: rs2567506; hg19: chr17-70715657;