12-104866587-TAA-T

Variant summary

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

The NM_001352171.3(SLC41A2):c.1028-10_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 0.217 in 1,290,512 control chromosomes in the GnomAD database, including 3,890 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.17 (3133 hom., cov: 0)
  • Exomes 𝑓: 0.22 (757 hom.)
• Consequence: SLC41A2 NM_001352171.3 splice_polypyrimidine_tract, intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.06

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-TAA-T is Benign according to our data. Variant chr12-104866587-TAA-T is described in ClinVar as [Benign]. Clinvar id is 1228903.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC41A2	NM_001352171.3	c.1028-10_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.1028-10_1028-9del		splice_polypyrimidine_tract_variant, intron_variant		1	NM_001352171.3	P1
	ENST00000671114.1	n.71-3559_71-3558del		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.167 AC: 23008 AN: 138160 Hom.: 3131 Cov.: 0

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.0347

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.0774

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0592

Gnomad OTH AF: 0.136

GnomAD3 exomes AF: 0.280 AC: 35111 AN: 125200 Hom.: 413 AF XY: 0.279 AC XY: 19377 AN XY: 69374

Gnomad AFR exome AF: 0.431

Gnomad AMR exome AF: 0.275

Gnomad ASJ exome AF: 0.297

Gnomad EAS exome AF: 0.287

Gnomad SAS exome AF: 0.243

Gnomad FIN exome AF: 0.260

Gnomad NFE exome AF: 0.268

Gnomad OTH exome AF: 0.280

GnomAD4 exome AF: 0.223 AC: 256901 AN: 1152322 Hom.: 757 AF XY: 0.224 AC XY: 128288 AN XY: 573546

Gnomad4 AFR exome AF: 0.415

Gnomad4 AMR exome AF: 0.266

Gnomad4 ASJ exome AF: 0.269

Gnomad4 EAS exome AF: 0.275

Gnomad4 SAS exome AF: 0.209

Gnomad4 FIN exome AF: 0.237

Gnomad4 NFE exome AF: 0.212

Gnomad4 OTH exome AF: 0.240

GnomAD4 genome AF: 0.167 AC: 23042 AN: 138190 Hom.: 3133 Cov.: 0 AF XY: 0.168 AC XY: 11197 AN XY: 66626

Gnomad4 AFR AF: 0.384

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.0774

Gnomad4 EAS AF: 0.254

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.111

Gnomad4 NFE AF: 0.0592

Gnomad4 OTH AF: 0.140

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;