12-104866587-TAAAAAAAAA-TAAAAAAAAAA

Variant names:

• chr12-104866587-T-TA
• rs34984157
• NM_001352171.3:c.1028-9dupT

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_001352171.3(SLC41A2):​c.1028-9dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0019 (1 hom., cov: 0)
  • Exomes 𝑓: 0.0049 (0 hom.)
• Consequence: SLC41A2 NM_001352171.3 intron
• Clinical Significance: Not reported in ClinVar
• 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]

ENSG00000286410 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC41A2	NM_001352171.3	c.1028-9dupT		intron_variant	Intron 6 of 10	ENST00000258538.8	NP_001339100.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC41A2	ENST00000258538.8	c.1028-9_1028-8insT		intron_variant	Intron 6 of 10	1	NM_001352171.3	ENSP00000258538.3
ENSG00000286410	ENST00000671114.1	n.71-3575_71-3574insA		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.00191 AC: 264 AN: 138218 Hom.: 1 Cov.: 0

Gnomad AFR AF: 0.00547

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00174

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000411

Gnomad SAS AF: 0.000926

Gnomad FIN AF: 0.000267

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000315

Gnomad OTH AF: 0.00214

GnomAD3 exomes AF: 0.00303 AC: 379 AN: 125200 Hom.: 0 AF XY: 0.00313 AC XY: 217 AN XY: 69374

Gnomad AFR exome AF: 0.00196

Gnomad AMR exome AF: 0.00450

Gnomad ASJ exome AF: 0.00413

Gnomad EAS exome AF: 0.00317

Gnomad SAS exome AF: 0.00342

Gnomad FIN exome AF: 0.00212

Gnomad NFE exome AF: 0.00270

Gnomad OTH exome AF: 0.00413

GnomAD4 exome AF: 0.00485 AC: 5817 AN: 1198896 Hom.: 0 Cov.: 0 AF XY: 0.00483 AC XY: 2881 AN XY: 596460

Gnomad4 AFR exome AF: 0.00490

Gnomad4 AMR exome AF: 0.00377

Gnomad4 ASJ exome AF: 0.00300

Gnomad4 EAS exome AF: 0.00251

Gnomad4 SAS exome AF: 0.00844

Gnomad4 FIN exome AF: 0.00445

Gnomad4 NFE exome AF: 0.00481

Gnomad4 OTH exome AF: 0.00446

GnomAD4 genome AF: 0.00192 AC: 266 AN: 138248 Hom.: 1 Cov.: 0 AF XY: 0.00206 AC XY: 137 AN XY: 66642

Gnomad4 AFR AF: 0.00551

Gnomad4 AMR AF: 0.00174

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000412

Gnomad4 SAS AF: 0.000932

Gnomad4 FIN AF: 0.000267

Gnomad4 NFE AF: 0.000315

Gnomad4 OTH AF: 0.00213

ClinVar

Not reported in ClinVar

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;