rs12582312

Variant names:

• chr12-104821402-C-T
• rs12582312
• NM_001352171.3:c.1537-16065G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001352171.3(SLC41A2):​c.1537-16065G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0245 in 152,068 control chromosomes in the GnomAD database, including 96 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 0.025 (96 hom., cov: 32)
• Consequence: SLC41A2 NM_001352171.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.277
• Publications: 2 publications found

Genes affected

SLC41A2 (HGNC:31045): (solute carrier family 41 member 2) Predicted to enable inorganic cation transmembrane transporter activity. Predicted to be involved in magnesium ion transmembrane transport. Predicted to act upstream of or within metal ion transport. Predicted to be integral component of membrane. Predicted to be active in plasma 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC41A2	NM_001352171.3	c.1537-16065G>A		intron_variant	Intron 10 of 10	ENST00000258538.8	NP_001339100.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC41A2	ENST00000258538.8	c.1537-16065G>A		intron_variant	Intron 10 of 10	1	NM_001352171.3	ENSP00000258538.3
SLC41A2	ENST00000549713.1	n.89+12689G>A		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.0245 AC: 3726 AN: 151950 Hom.: 96 Cov.: 32

Gnomad AFR AF: 0.0399

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0213

Gnomad ASJ AF: 0.0127

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.0147

Gnomad FIN AF: 0.00503

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0103

Gnomad OTH AF: 0.0274

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

GnomAD4 genome AF: 0.0245 AC: 3727 AN: 152068 Hom.: 96 Cov.: 32 AF XY: 0.0247 AC XY: 1834 AN XY: 74328

African (AFR) AF: 0.0398 AC: 1652 AN: 41478

American (AMR) AF: 0.0213 AC: 325 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0127 AC: 44 AN: 3468

East Asian (EAS) AF: 0.153 AC: 793 AN: 5180

South Asian (SAS) AF: 0.0149 AC: 72 AN: 4818

European-Finnish (FIN) AF: 0.00503 AC: 53 AN: 10544

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0103 AC: 703 AN: 67998

Other (OTH) AF: 0.0295 AC: 62 AN: 2104

Alfa AF: 0.0181 Hom.: 4

Bravo AF: 0.0292

Asia WGS AF: 0.0630 AC: 220 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.1
DANN	Benign	0.75
PhyloP100		0.28
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: rs12582312; hg19: chr12-105215180;