rs2478571

chr10-17993498-G-A

Variant summary

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

The NM_001145195.2(SLC39A12):c.1533+207G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 152,192 control chromosomes in the GnomAD database, including 5,383 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 0.24 (5383 hom., cov: 33)
• Consequence: SLC39A12 NM_001145195.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0510

Genes affected

SLC39A12 (HGNC:20860): (solute carrier family 39 member 12) Zinc is an essential cofactor for hundreds of enzymes. It is involved in protein, nucleic acid, carbohydrate, and lipid metabolism, as well as in the control of gene transcription, growth, development, and differentiation. SLC39A12 belongs to a subfamily of proteins that show structural characteristics of zinc transporters (Taylor and Nicholson, 2003 [PubMed 12659941]).[supplied by OMIM, Aug 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.359 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC39A12	NM_001145195.2	c.1533+207G>A		intron_variant		ENST00000377369.7
SLC39A12	NM_001282733.2	c.1530+207G>A		intron_variant
SLC39A12	NM_001282734.2	c.1131+207G>A		intron_variant
SLC39A12	NM_152725.4	c.1423-2158G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC39A12	ENST00000377369.7	c.1533+207G>A		intron_variant		1	NM_001145195.2	A1
SLC39A12	ENST00000377371.3	c.1530+207G>A		intron_variant		1		P4
SLC39A12	ENST00000377374.8	c.1423-2158G>A		intron_variant		2
SLC39A12	ENST00000539911.5	c.1131+207G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36594 AN: 152074 Hom.: 5379 Cov.: 33

Gnomad AFR AF: 0.0679

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.240 AC: 36589 AN: 152192 Hom.: 5383 Cov.: 33 AF XY: 0.246 AC XY: 18279 AN XY: 74402

Gnomad4 AFR AF: 0.0677

Gnomad4 AMR AF: 0.367

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.310

Gnomad4 SAS AF: 0.312

Gnomad4 FIN AF: 0.293

Gnomad4 NFE AF: 0.297

Gnomad4 OTH AF: 0.252

Alfa AF: 0.276 Hom.: 3309

Bravo AF: 0.237

Asia WGS AF: 0.302 AC: 1048 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	2.0
Dann	Benign	0.54

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: rs2478571; hg19: chr10-18282427;