Genetic Variant SLC41A2:c.1028-9dupT (chr12-104866587-T-TA) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 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

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.272

Publications

1 publications found

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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001352171.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SLC41A2	NM_001352171.3	MANE Select	c.1028-9dupT	intron	N/A	NP_001339100.1	Q96JW4
SLC41A2	NM_001352169.2		c.1028-9dupT	intron	N/A	NP_001339098.1	Q96JW4
SLC41A2	NM_001352170.3		c.1028-9dupT	intron	N/A	NP_001339099.1	Q96JW4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SLC41A2	ENST00000258538.8	TSL:1 MANE Select	c.1028-9_1028-8insT	intron	N/A	ENSP00000258538.3	Q96JW4
SLC41A2	ENST00000906846.1		c.1028-9_1028-8insT	intron	N/A	ENSP00000576905.1
SLC41A2	ENST00000906847.1		c.1028-9_1028-8insT	intron	N/A	ENSP00000576906.1

Frequencies

GnomAD3 genomes

AF:

0.00191

AC:

264

AN:

138218

Hom.:

Cov.:

show subpopulations

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

GnomAD2 exomes

AF:

0.00303

AC:

379

AN:

125200

AF XY:

0.00313

show subpopulations

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 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.:

Cov.:

AF XY:

0.00483

AC XY:

2881

AN XY:

596460

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.00490

AC:

131

AN:

26740

American (AMR)

AF:

0.00377

AC:

102

AN:

27058

Ashkenazi Jewish (ASJ)

AF:

0.00300

AC:

AN:

20364

East Asian (EAS)

AF:

0.00251

AC:

AN:

36302

South Asian (SAS)

AF:

0.00844

AC:

522

AN:

61826

European-Finnish (FIN)

AF:

0.00445

AC:

160

AN:

35988

Middle Eastern (MID)

AF:

0.00499

AC:

AN:

4010

European-Non Finnish (NFE)

AF:

0.00481

AC:

4509

AN:

937052

Other (OTH)

AF:

0.00446

AC:

221

AN:

49556

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.284

Heterozygous variant carriers

504

1007

1511

2014

2518

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

184

368

552

736

920

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00192

AC:

266

AN:

138248

Hom.:

Cov.:

AF XY:

0.00206

AC XY:

137

AN XY:

66642

show subpopulations

African (AFR)

AF:

0.00551

AC:

210

AN:

38126

American (AMR)

AF:

0.00174

AC:

AN:

13780

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3296

East Asian (EAS)

AF:

0.000412

AC:

AN:

4850

South Asian (SAS)

AF:

0.000932

AC:

AN:

4292

European-Finnish (FIN)

AF:

0.000267

AC:

AN:

7478

Middle Eastern (MID)

AF:

0.00

AC:

AN:

248

European-Non Finnish (NFE)

AF:

0.000315

AC:

AN:

63460

Other (OTH)

AF:

0.00213

AC:

AN:

1882

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.485

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.27

Mutation Taster

=100/0

polymorphism

(source)

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

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12-104866587-TAAAAAAAAA-TAAAAAAAAAA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over