chr17-72717400-G-A

Variant names:

• chr17-72717400-G-A
• rs891684
• NM_139177.4:c.671+19250C>T

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+19250C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 152,018 control chromosomes in the GnomAD database, including 1,197 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 0.10 (1197 hom., cov: 32)
• Consequence: SLC39A11 NM_139177.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0660
• Publications: 7 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 (AFR) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_139177.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC39A11	NM_139177.4	MANE Select	c.671+19250C>T		intron	N/A	NP_631916.2
	SLC39A11	NM_001159770.2		c.692+19250C>T		intron	N/A	NP_001153242.1
	SLC39A11	NM_001352692.2		c.692+19250C>T		intron	N/A	NP_001339621.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC39A11	ENST00000255559.8	TSL:1 MANE Select	c.671+19250C>T		intron	N/A	ENSP00000255559.3
	SLC39A11	ENST00000542342.6	TSL:2	c.692+19250C>T		intron	N/A	ENSP00000445829.2
	SLC39A11	ENST00000582769.5	TSL:5	c.419+19250C>T		intron	N/A	ENSP00000463467.1

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15749 AN: 151898 Hom.: 1192 Cov.: 32

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.0188

Gnomad AMR AF: 0.0847

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.0758

Gnomad FIN AF: 0.0468

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0488

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.104 AC: 15783 AN: 152018 Hom.: 1197 Cov.: 32 AF XY: 0.103 AC XY: 7618 AN XY: 74298

African (AFR) AF: 0.213 AC: 8832 AN: 41446

American (AMR) AF: 0.0846 AC: 1291 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 553 AN: 3470

East Asian (EAS) AF: 0.129 AC: 665 AN: 5138

South Asian (SAS) AF: 0.0759 AC: 366 AN: 4822

European-Finnish (FIN) AF: 0.0468 AC: 496 AN: 10592

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0488 AC: 3319 AN: 67976

Other (OTH) AF: 0.103 AC: 217 AN: 2106

Alfa AF: 0.0383 Hom.: 51

Bravo AF: 0.113

Asia WGS AF: 0.107 AC: 374 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.3
DANN	Benign	0.24
PhyloP100		0.066
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs891684; hg19: chr17-70713539;