rs2468339

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
SLC41A2	NM_001352171.3	c.1537-5962T>C		intron_variant		ENST00000258538.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC41A2	ENST00000258538.8	c.1537-5962T>C		intron_variant		1	NM_001352171.3	P1
SLC41A2	ENST00000549713.1	n.90-5962T>C		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.371

Gnomad4 AMR AF: 0.546

Gnomad4 ASJ AF: 0.666

Gnomad4 EAS AF: 0.252

Gnomad4 SAS AF: 0.363

Gnomad4 FIN AF: 0.503

Gnomad4 NFE AF: 0.564

Gnomad4 OTH AF: 0.535

Alfa AF: 0.383 Hom.: 1010

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

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: rs2468339; hg19: chr12-105205077;