12-104866587-TA-T

Position:

• chr12-104866587-TA-T

Variant summary

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

The NM_001352171.3(SLC41A2):​c.1028-9del variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.55 (20562 hom., cov: 0)
  • Exomes 𝑓: 0.42 (4484 hom.)
  • Failed GnomAD Quality Control
• Consequence: SLC41A2 NM_001352171.3 splice_polypyrimidine_tract, intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.272

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 12-104866587-TA-T is Benign according to our data. Variant chr12-104866587-TA-T is described in ClinVar as [Benign]. Clinvar id is 1270186.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.601 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC41A2	NM_001352171.3	c.1028-9del		splice_polypyrimidine_tract_variant, intron_variant		ENST00000258538.8	NP_001339100.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC41A2	ENST00000258538.8	c.1028-9del		splice_polypyrimidine_tract_variant, intron_variant		1	NM_001352171.3	ENSP00000258538	P1
	ENST00000671114.1	n.71-3558del		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.550 AC: 75930 AN: 137986 Hom.: 20566 Cov.: 0

Gnomad AFR AF: 0.486

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.589

GnomAD3 exomes AF: 0.371 AC: 46449 AN: 125200 Hom.: 756 AF XY: 0.371 AC XY: 25772 AN XY: 69374

Gnomad AFR exome AF: 0.302

Gnomad AMR exome AF: 0.365

Gnomad ASJ exome AF: 0.394

Gnomad EAS exome AF: 0.265

Gnomad SAS exome AF: 0.341

Gnomad FIN exome AF: 0.378

Gnomad NFE exome AF: 0.405

Gnomad OTH exome AF: 0.391

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.424 AC: 502601 AN: 1184254 Hom.: 4484 Cov.: 0 AF XY: 0.422 AC XY: 248975 AN XY: 589294

Gnomad4 AFR exome AF: 0.344

Gnomad4 AMR exome AF: 0.374

Gnomad4 ASJ exome AF: 0.423

Gnomad4 EAS exome AF: 0.293

Gnomad4 SAS exome AF: 0.367

Gnomad4 FIN exome AF: 0.394

Gnomad4 NFE exome AF: 0.438

Gnomad4 OTH exome AF: 0.420

GnomAD4 genome AF: 0.550 AC: 75938 AN: 138014 Hom.: 20562 Cov.: 0 AF XY: 0.544 AC XY: 36199 AN XY: 66542

Gnomad4 AFR AF: 0.486

Gnomad4 AMR AF: 0.570

Gnomad4 ASJ AF: 0.652

Gnomad4 EAS AF: 0.322

Gnomad4 SAS AF: 0.431

Gnomad4 FIN AF: 0.524

Gnomad4 NFE AF: 0.606

Gnomad4 OTH AF: 0.585

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 04, 2021

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs34984157; hg19: chr12-105260365;