rs10861279

Variant names:

• chr12-104821412-A-C
• rs10861279
• NM_001352171.3:c.1537-16075T>G

Your query was ambiguous. Multiple possible variants found:

• chr12-104821412-A-C
• chr12-104821412-A-G

Variant summary

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

The NM_001352171.3(SLC41A2):​c.1537-16075T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0868 in 152,212 control chromosomes in the GnomAD database, including 636 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 0.087 (636 hom., cov: 32)
• Consequence: SLC41A2 NM_001352171.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.35
• Publications: 4 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 (SAS) allele frequency at 95% confidence interval = 0.0984 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC41A2	NM_001352171.3	c.1537-16075T>G		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.1537-16075T>G		intron_variant	Intron 10 of 10	1	NM_001352171.3	ENSP00000258538.3
SLC41A2	ENST00000549713.1	n.89+12679T>G		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.0868 AC: 13200 AN: 152094 Hom.: 635 Cov.: 32

Gnomad AFR AF: 0.0823

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.0626

Gnomad ASJ AF: 0.0573

Gnomad EAS AF: 0.0825

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.0772

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0968

Gnomad OTH AF: 0.0882

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

GnomAD4 genome AF: 0.0868 AC: 13211 AN: 152212 Hom.: 636 Cov.: 32 AF XY: 0.0862 AC XY: 6411 AN XY: 74414

African (AFR) AF: 0.0823 AC: 3419 AN: 41530

American (AMR) AF: 0.0626 AC: 956 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0573 AC: 199 AN: 3472

East Asian (EAS) AF: 0.0827 AC: 429 AN: 5188

South Asian (SAS) AF: 0.106 AC: 511 AN: 4822

European-Finnish (FIN) AF: 0.0772 AC: 818 AN: 10592

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0968 AC: 6583 AN: 68012

Other (OTH) AF: 0.0897 AC: 189 AN: 2108

Alfa AF: 0.0625 Hom.: 83

Bravo AF: 0.0848

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.8
DANN	Benign	0.80
PhyloP100		1.4
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: rs10861279; hg19: chr12-105215190;