12-104866381-TACAC-T

Variant summary

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

The NM_001352171.3(SLC41A2):c.1175+47_1175+50del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0204 in 1,414,436 control chromosomes in the GnomAD database, including 97 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.024 (56 hom., cov: 0)
  • Exomes 𝑓: 0.020 (41 hom.)
• Consequence: SLC41A2 NM_001352171.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.25

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 12-104866381-TACAC-T is Benign according to our data. Variant chr12-104866381-TACAC-T is described in ClinVar as [Benign]. Clinvar id is 1179931.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC41A2	NM_001352171.3	c.1175+47_1175+50del		intron_variant		ENST00000258538.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC41A2	ENST00000258538.8	c.1175+47_1175+50del		intron_variant		1	NM_001352171.3	P1
	ENST00000671114.1	n.71-3749_71-3746del		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0243 AC: 3428 AN: 140950 Hom.: 54 Cov.: 0

Gnomad AFR AF: 0.0248

Gnomad AMI AF: 0.00694

Gnomad AMR AF: 0.0338

Gnomad ASJ AF: 0.0159

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.0360

Gnomad FIN AF: 0.0280

Gnomad MID AF: 0.0240

Gnomad NFE AF: 0.0142

Gnomad OTH AF: 0.0228

GnomAD3 exomes AF: 0.0336 AC: 5080 AN: 151248 Hom.: 30 AF XY: 0.0315 AC XY: 2595 AN XY: 82436

Gnomad AFR exome AF: 0.0322

Gnomad AMR exome AF: 0.0558

Gnomad ASJ exome AF: 0.0135

Gnomad EAS exome AF: 0.105

Gnomad SAS exome AF: 0.0326

Gnomad FIN exome AF: 0.0284

Gnomad NFE exome AF: 0.0186

Gnomad OTH exome AF: 0.0246

GnomAD4 exome AF: 0.0199 AC: 25403 AN: 1273394 Hom.: 41 AF XY: 0.0201 AC XY: 12609 AN XY: 625838

Gnomad4 AFR exome AF: 0.0255

Gnomad4 AMR exome AF: 0.0486

Gnomad4 ASJ exome AF: 0.0140

Gnomad4 EAS exome AF: 0.127

Gnomad4 SAS exome AF: 0.0321

Gnomad4 FIN exome AF: 0.0251

Gnomad4 NFE exome AF: 0.0142

Gnomad4 OTH exome AF: 0.0234

GnomAD4 genome AF: 0.0244 AC: 3443 AN: 141042 Hom.: 56 Cov.: 0 AF XY: 0.0255 AC XY: 1750 AN XY: 68642

Gnomad4 AFR AF: 0.0248

Gnomad4 AMR AF: 0.0343

Gnomad4 ASJ AF: 0.0159

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.0358

Gnomad4 FIN AF: 0.0280

Gnomad4 NFE AF: 0.0142

Gnomad4 OTH AF: 0.0252

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 18, 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: rs57548373; hg19: chr12-105260159;