Genetic Variant SLC41A2:c.1175+49_1175+50dupGT (chr12-104866381-T-TAC) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001387131.1(SLC41A2):c.1224_1225dupGT(p.Tyr409CysfsTer19) variant causes a frameshift 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 0.034 ( 85 hom., cov: 0)

Exomes 𝑓: 0.024 ( 10 hom. )

Consequence

SLC41A2
NM_001387131.1 frameshift

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.602

Variant links:

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]

SLC41A2 links:

ENSG00000286410 (HGNC:):

ENSG00000286410 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0672 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC41A2	NM_001352171.3 link	c.1175+49_1175+50dupGT		intron_variant	Intron 7 of 10	ENST00000258538.8	NP_001339100.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC41A2	ENST00000258538.8 link	c.1175+50_1175+51insGT		intron_variant	Intron 7 of 10	1	NM_001352171.3	ENSP00000258538.3		Q96JW4
ENSG00000286410	ENST00000671114.1 link	n.71-3781_71-3780insAC		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.0341

AC:

4808

AN:

140926

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0462

Gnomad AMI

AF:

0.00347

Gnomad AMR

AF:

0.0226

Gnomad ASJ

AF:

0.0551

Gnomad EAS

AF:

0.0155

Gnomad SAS

AF:

0.0745

Gnomad FIN

AF:

0.0265

Gnomad MID

AF:

0.0342

Gnomad NFE

AF:

0.0292

Gnomad OTH

AF:

0.0280

GnomAD3 exomes

AF:

0.0219

AC:

3312

AN:

151248

Hom.:

AF XY:

0.0228

AC XY:

1880

AN XY:

82436

show subpopulations

Gnomad AFR exome

AF:

0.0334

Gnomad AMR exome

AF:

0.0107

Gnomad ASJ exome

AF:

0.0329

Gnomad EAS exome

AF:

0.0107

Gnomad SAS exome

AF:

0.0426

Gnomad FIN exome

AF:

0.0194

Gnomad NFE exome

AF:

0.0199

Gnomad OTH exome

AF:

0.0232

GnomAD4 exome

AF:

0.0239

AC:

30508

AN:

1278850

Hom.:

Cov.:

AF XY:

0.0241

AC XY:

15160

AN XY:

628574

show subpopulations

Gnomad4 AFR exome

AF:

0.0393

Gnomad4 AMR exome

AF:

0.0119

Gnomad4 ASJ exome

AF:

0.0440

Gnomad4 EAS exome

AF:

0.0111

Gnomad4 SAS exome

AF:

0.0446

Gnomad4 FIN exome

AF:

0.0243

Gnomad4 NFE exome

AF:

0.0225

Gnomad4 OTH exome

AF:

0.0268

GnomAD4 genome

AF:

0.0342

AC:

4821

AN:

141018

Hom.:

Cov.:

AF XY:

0.0353

AC XY:

2420

AN XY:

68620

show subpopulations

Gnomad4 AFR

AF:

0.0465

Gnomad4 AMR

AF:

0.0225

Gnomad4 ASJ

AF:

0.0551

Gnomad4 EAS

AF:

0.0155

Gnomad4 SAS

AF:

0.0739

Gnomad4 FIN

AF:

0.0265

Gnomad4 NFE

AF:

0.0292

Gnomad4 OTH

AF:

0.0277

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over