12-104866415-CAT-C

Variant summary

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

The NM_001352171.3(SLC41A2):c.1175+15_1175+16del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00573 in 1,530,446 control chromosomes in the GnomAD database, including 250 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.035 (231 hom., cov: 28)
  • Exomes 𝑓: 0.0029 (19 hom.)
• Consequence: SLC41A2 NM_001352171.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.02

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 12-104866415-CAT-C is Benign according to our data. Variant chr12-104866415-CAT-C is described in ClinVar as [Benign]. Clinvar id is 1228445.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC41A2	NM_001352171.3	c.1175+15_1175+16del		intron_variant		ENST00000258538.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC41A2	ENST00000258538.8	c.1175+15_1175+16del		intron_variant		1	NM_001352171.3	P1
	ENST00000671114.1	n.71-3744_71-3743del		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0348 AC: 4766 AN: 136944 Hom.: 232 Cov.: 28

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0156

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000223

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0105

Gnomad NFE AF: 0.000612

Gnomad OTH AF: 0.0231

GnomAD3 exomes AF: 0.00793 AC: 1594 AN: 200884 Hom.: 57 AF XY: 0.00589 AC XY: 643 AN XY: 109172

Gnomad AFR exome AF: 0.0835

Gnomad AMR exome AF: 0.00633

Gnomad ASJ exome AF: 0.00417

Gnomad EAS exome AF: 0.0000633

Gnomad SAS exome AF: 0.00149

Gnomad FIN exome AF: 0.00261

Gnomad NFE exome AF: 0.00203

Gnomad OTH exome AF: 0.00577

GnomAD4 exome AF: 0.00286 AC: 3991 AN: 1393396 Hom.: 19 AF XY: 0.00253 AC XY: 1748 AN XY: 692274

Gnomad4 AFR exome AF: 0.0934

Gnomad4 AMR exome AF: 0.00726

Gnomad4 ASJ exome AF: 0.00194

Gnomad4 EAS exome AF: 0.0000526

Gnomad4 SAS exome AF: 0.00127

Gnomad4 FIN exome AF: 0.00146

Gnomad4 NFE exome AF: 0.000570

Gnomad4 OTH exome AF: 0.00627

GnomAD4 genome AF: 0.0349 AC: 4780 AN: 137050 Hom.: 231 Cov.: 28 AF XY: 0.0332 AC XY: 2216 AN XY: 66704

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.0156

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000223

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000612

Gnomad4 OTH AF: 0.0228

Alfa AF: 0.000503 Hom.: 0

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 20, 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: rs757344904; hg19: chr12-105260193;