12-104821412-A-C

Position:

• chr12-104821412-A-C

Variant summary

Our verdict is Benign. Variant got -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

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 (SAS) allele frequency at 95% confidence interval = 0.0984 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC41A2	NM_001352171.3	c.1537-16075T>G		intron_variant		ENST00000258538.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC41A2	ENST00000258538.8	c.1537-16075T>G		intron_variant		1	NM_001352171.3	P1
SLC41A2	ENST00000549713.1	n.89+12679T>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.0823

Gnomad4 AMR AF: 0.0626

Gnomad4 ASJ AF: 0.0573

Gnomad4 EAS AF: 0.0827

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.0772

Gnomad4 NFE AF: 0.0968

Gnomad4 OTH AF: 0.0897

Alfa AF: 0.0619 Hom.: 79

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

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: rs10861279; hg19: chr12-105215190;