12-104866587-TAAA-T

Variant summary

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

The NM_001352171.3(SLC41A2):c.1028-11_1028-9del variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0339 in 1,308,236 control chromosomes in the GnomAD database, including 71 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0092 (33 hom., cov: 0)
  • Exomes 𝑓: 0.037 (38 hom.)
• Consequence: SLC41A2 NM_001352171.3 splice_polypyrimidine_tract, intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.82

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-TAAA-T is Benign according to our data. Variant chr12-104866587-TAAA-T is described in ClinVar as [Benign]. Clinvar id is 1286792.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC41A2	NM_001352171.3	c.1028-11_1028-9del		splice_polypyrimidine_tract_variant, intron_variant		ENST00000258538.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC41A2	ENST00000258538.8	c.1028-11_1028-9del		splice_polypyrimidine_tract_variant, intron_variant		1	NM_001352171.3	P1
	ENST00000671114.1	n.71-3560_71-3558del		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.00914 AC: 1263 AN: 138188 Hom.: 32 Cov.: 0

Gnomad AFR AF: 0.00221

Gnomad AMI AF: 0.00598

Gnomad AMR AF: 0.0208

Gnomad ASJ AF: 0.000607

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.0153

Gnomad FIN AF: 0.00831

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00246

Gnomad OTH AF: 0.0113

GnomAD3 exomes AF: 0.0719 AC: 9007 AN: 125200 Hom.: 23 AF XY: 0.0691 AC XY: 4793 AN XY: 69374

Gnomad AFR exome AF: 0.106

Gnomad AMR exome AF: 0.101

Gnomad ASJ exome AF: 0.0653

Gnomad EAS exome AF: 0.178

Gnomad SAS exome AF: 0.0685

Gnomad FIN exome AF: 0.0499

Gnomad NFE exome AF: 0.0462

Gnomad OTH exome AF: 0.0613

GnomAD4 exome AF: 0.0368 AC: 43094 AN: 1170016 Hom.: 38 AF XY: 0.0378 AC XY: 21981 AN XY: 581992

Gnomad4 AFR exome AF: 0.0864

Gnomad4 AMR exome AF: 0.0877

Gnomad4 ASJ exome AF: 0.0460

Gnomad4 EAS exome AF: 0.182

Gnomad4 SAS exome AF: 0.0515

Gnomad4 FIN exome AF: 0.0443

Gnomad4 NFE exome AF: 0.0265

Gnomad4 OTH exome AF: 0.0437

GnomAD4 genome AF: 0.00920 AC: 1271 AN: 138220 Hom.: 33 Cov.: 0 AF XY: 0.0102 AC XY: 681 AN XY: 66628

Gnomad4 AFR AF: 0.00228

Gnomad4 AMR AF: 0.0211

Gnomad4 ASJ AF: 0.000607

Gnomad4 EAS AF: 0.120

Gnomad4 SAS AF: 0.0154

Gnomad4 FIN AF: 0.00831

Gnomad4 NFE AF: 0.00246

Gnomad4 OTH AF: 0.0112

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

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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: rs34984157; hg19: chr12-105260365;