rs8068946

Positions:

• chr17-72716374-G-A
• chr17-72716374-G-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000255559.8(SLC39A11):​c.671+20276C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.481 in 151,572 control chromosomes in the GnomAD database, including 22,027 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 0.48 (22027 hom., cov: 30)
• Consequence: SLC39A11 ENST00000255559.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.415

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.859 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC39A11	NM_139177.4	c.671+20276C>T		intron_variant		ENST00000255559.8	NP_631916.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC39A11	ENST00000255559.8	c.671+20276C>T		intron_variant		1	NM_139177.4	ENSP00000255559	P4

Frequencies

GnomAD3 genomes AF: 0.481 AC: 72863 AN: 151454 Hom.: 21965 Cov.: 30

Gnomad AFR AF: 0.866

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.481 AC: 72979 AN: 151572 Hom.: 22027 Cov.: 30 AF XY: 0.476 AC XY: 35220 AN XY: 73996

Gnomad4 AFR AF: 0.866

Gnomad4 AMR AF: 0.374

Gnomad4 ASJ AF: 0.446

Gnomad4 EAS AF: 0.333

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.295

Gnomad4 NFE AF: 0.335

Gnomad4 OTH AF: 0.450

Alfa AF: 0.353 Hom.: 17173

Bravo AF: 0.508

Asia WGS AF: 0.313 AC: 1089 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	17
DANN	Benign	0.90

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: rs8068946; hg19: chr17-70712513;