rs2452924

Positions:

• chr17-72927624-T-C
• chr17-72927624-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_139177.4(SLC39A11):​c.430+20128A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 151,992 control chromosomes in the GnomAD database, including 9,276 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 0.34 (9276 hom., cov: 32)
• Consequence: SLC39A11 NM_139177.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC39A11	NM_139177.4	c.430+20128A>G		intron_variant		ENST00000255559.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC39A11	ENST00000255559.8	c.430+20128A>G		intron_variant		1	NM_139177.4	P4

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51128 AN: 151874 Hom.: 9262 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.337 AC: 51151 AN: 151992 Hom.: 9276 Cov.: 32 AF XY: 0.341 AC XY: 25290 AN XY: 74272

Gnomad4 AFR AF: 0.202

Gnomad4 AMR AF: 0.443

Gnomad4 ASJ AF: 0.320

Gnomad4 EAS AF: 0.397

Gnomad4 SAS AF: 0.331

Gnomad4 FIN AF: 0.408

Gnomad4 NFE AF: 0.380

Gnomad4 OTH AF: 0.357

Alfa AF: 0.375 Hom.: 13924

Bravo AF: 0.335

Asia WGS AF: 0.361 AC: 1254 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.11
DANN	Benign	0.56
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs2452924; hg19: chr17-70923763;