12-104856304-G-C

Variant names:

• chr12-104856304-G-C
• rs10507183
• NM_001352171.3:c.1255+4987C>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.1255+4987C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.487 in 151,866 control chromosomes in the GnomAD database, including 18,887 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 (18887 hom., cov: 31)
• Consequence: SLC41A2 NM_001352171.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310
• 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=-0.91).
• 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.1255+4987C>G		intron_variant	Intron 8 of 10	ENST00000258538.8	NP_001339100.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC41A2	ENST00000258538.8	c.1255+4987C>G		intron_variant	Intron 8 of 10	1	NM_001352171.3	ENSP00000258538.3

Frequencies

GnomAD3 genomes AF: 0.488 AC: 73999 AN: 151748 Hom.: 18883 Cov.: 31

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.667

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.502

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.487 AC: 74020 AN: 151866 Hom.: 18887 Cov.: 31 AF XY: 0.483 AC XY: 35845 AN XY: 74220

African (AFR) AF: 0.365 AC: 15112 AN: 41440

American (AMR) AF: 0.542 AC: 8282 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.667 AC: 2313 AN: 3470

East Asian (EAS) AF: 0.247 AC: 1277 AN: 5176

South Asian (SAS) AF: 0.364 AC: 1754 AN: 4820

European-Finnish (FIN) AF: 0.502 AC: 5259 AN: 10484

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

European-Non Finnish (NFE) AF: 0.563 AC: 38252 AN: 67896

Other (OTH) AF: 0.529 AC: 1113 AN: 2104

Alfa AF: 0.518 Hom.: 1901

Bravo AF: 0.490

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.0
DANN	Benign	0.25
PhyloP100		-0.031
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: rs10507183; hg19: chr12-105250082;