rs891684

chr17-72717400-G-Achr17-72717400-G-C

Variant summary

Our verdict is Benign. Variant got -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

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC39A11	NM_139177.4	c.671+19250C>T		intron_variant		ENST00000255559.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC39A11	ENST00000255559.8	c.671+19250C>T		intron_variant		1	NM_139177.4	P4

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

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.0846

Gnomad4 ASJ AF: 0.159

Gnomad4 EAS AF: 0.129

Gnomad4 SAS AF: 0.0759

Gnomad4 FIN AF: 0.0468

Gnomad4 NFE AF: 0.0488

Gnomad4 OTH AF: 0.103

Alfa AF: 0.0305 Hom.: 30

Bravo AF: 0.113

Asia WGS AF: 0.107 AC: 374 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	3.3
Dann	Benign	0.24

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: rs891684; hg19: chr17-70713539;