rs2468339

Variant names:

• chr12-104811299-A-G
• rs2468339
• NM_001352171.3:c.1537-5962T>C

Your query was ambiguous. Multiple possible variants found:

• chr12-104811299-A-G
• chr12-104811299-A-T

Variant summary

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

The NM_001352171.3(SLC41A2):​c.1537-5962T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.49 in 152,116 control chromosomes in the GnomAD database, including 19,120 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 0.49 (19120 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]

ENSG00000309266 (HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC41A2	NM_001352171.3	c.1537-5962T>C		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.1537-5962T>C		intron_variant	Intron 10 of 10	1	NM_001352171.3	ENSP00000258538.3
SLC41A2	ENST00000549713.1	n.90-5962T>C		intron_variant	Intron 1 of 1	3
ENSG00000309266	ENST00000839921.1	n.200-1299A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.490 AC: 74541 AN: 151998 Hom.: 19115 Cov.: 32

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.540

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.490 AC: 74562 AN: 152116 Hom.: 19120 Cov.: 32 AF XY: 0.486 AC XY: 36112 AN XY: 74344

African (AFR) AF: 0.371 AC: 15399 AN: 41498

American (AMR) AF: 0.546 AC: 8346 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.666 AC: 2312 AN: 3472

East Asian (EAS) AF: 0.252 AC: 1304 AN: 5176

South Asian (SAS) AF: 0.363 AC: 1754 AN: 4828

European-Finnish (FIN) AF: 0.503 AC: 5320 AN: 10574

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.564 AC: 38338 AN: 67972

Other (OTH) AF: 0.535 AC: 1131 AN: 2114

Alfa AF: 0.384 Hom.: 1076

Bravo AF: 0.493

Asia WGS AF: 0.320 AC: 1113 AN: 3476

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	0.62
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: rs2468339; hg19: chr12-105205077;