12-104866367-AAGAC-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001352171.3(SLC41A2):c.1175+61_1175+64del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0196 in 1,446,224 control chromosomes in the GnomAD database, including 775 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.051 (351 hom., cov: 30)
  • Exomes 𝑓: 0.016 (424 hom.)
• Consequence: SLC41A2 NM_001352171.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.342

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 12-104866367-AAGAC-A is Benign according to our data. Variant chr12-104866367-AAGAC-A is described in ClinVar as [Benign]. Clinvar id is 1290088.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC41A2	NM_001352171.3	c.1175+61_1175+64del		intron_variant		ENST00000258538.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC41A2	ENST00000258538.8	c.1175+61_1175+64del		intron_variant		1	NM_001352171.3	P1
	ENST00000671114.1	n.71-3786_71-3783del		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0510 AC: 7053 AN: 138316 Hom.: 352 Cov.: 30

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.00920

Gnomad AMR AF: 0.0276

Gnomad ASJ AF: 0.0229

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00764

Gnomad FIN AF: 0.0144

Gnomad MID AF: 0.0359

Gnomad NFE AF: 0.0155

Gnomad OTH AF: 0.0391

GnomAD4 exome AF: 0.0163 AC: 21277 AN: 1307790 Hom.: 424 AF XY: 0.0155 AC XY: 9965 AN XY: 641782

Gnomad4 AFR exome AF: 0.138

Gnomad4 AMR exome AF: 0.0136

Gnomad4 ASJ exome AF: 0.0255

Gnomad4 EAS exome AF: 0.0000525

Gnomad4 SAS exome AF: 0.00781

Gnomad4 FIN exome AF: 0.0142

Gnomad4 NFE exome AF: 0.0135

Gnomad4 OTH exome AF: 0.0210

GnomAD4 genome AF: 0.0511 AC: 7069 AN: 138434 Hom.: 351 Cov.: 30 AF XY: 0.0498 AC XY: 3328 AN XY: 66806

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.0276

Gnomad4 ASJ AF: 0.0229

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00765

Gnomad4 FIN AF: 0.0144

Gnomad4 NFE AF: 0.0155

Gnomad4 OTH AF: 0.0387

Alfa AF: 0.0287 Hom.: 13

Asia WGS AF: 0.0110 AC: 37 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 15, 2021

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Computational scores

Source: dbNSFP v4.3

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: rs139689401; hg19: chr12-105260145;