Genetic Variant SLC41A2:c.1028-9delT (chr12-104866587-TA-T) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001352171.3(SLC41A2):c.1028-9delT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.55 ( 20562 hom., cov: 0)

Exomes 𝑓: 0.42 ( 4484 hom. )

Failed GnomAD Quality Control

Consequence

SLC41A2
NM_001352171.3 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

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: Benign. The variant received -10 ACMG points.

BP6

Variant 12-104866587-TA-T is Benign according to our data. Variant chr12-104866587-TA-T is described in ClinVar as Benign. ClinVar VariationId is 1270186.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.601 is higher than 0.05.

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.1028-9delT	intron	N/A	NP_001339100.1	Q96JW4
SLC41A2	NM_001352169.2		c.1028-9delT	intron	N/A	NP_001339098.1	Q96JW4
SLC41A2	NM_001352170.3		c.1028-9delT	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.1028-9delT	intron	N/A	ENSP00000258538.3	Q96JW4
SLC41A2	ENST00000906846.1		c.1028-9delT	intron	N/A	ENSP00000576905.1
SLC41A2	ENST00000906847.1		c.1028-9delT	intron	N/A	ENSP00000576906.1

Frequencies

GnomAD3 genomes

AF:

0.550

AC:

75930

AN:

137986

Hom.:

20566

Cov.:

show subpopulations

Gnomad AFR

AF:

0.486

Gnomad AMI

AF:

0.571

Gnomad AMR

AF:

0.570

Gnomad ASJ

AF:

0.652

Gnomad EAS

AF:

0.323

Gnomad SAS

AF:

0.430

Gnomad FIN

AF:

0.524

Gnomad MID

AF:

0.620

Gnomad NFE

AF:

0.606

Gnomad OTH

AF:

0.589

GnomAD2 exomes

AF:

0.371

AC:

46449

AN:

125200

AF XY:

0.371

show subpopulations

Gnomad AFR exome

AF:

0.302

Gnomad AMR exome

AF:

0.365

Gnomad ASJ exome

AF:

0.394

Gnomad EAS exome

AF:

0.265

Gnomad FIN exome

AF:

0.378

Gnomad NFE exome

AF:

0.405

Gnomad OTH exome

AF:

0.391

GnomAD4 exome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.424

AC:

502601

AN:

1184254

Hom.:

4484

Cov.:

AF XY:

0.422

AC XY:

248975

AN XY:

589294

show subpopulations

African (AFR)

AF:

0.344

AC:

8966

AN:

26098

American (AMR)

AF:

0.374

AC:

9996

AN:

26694

Ashkenazi Jewish (ASJ)

AF:

0.423

AC:

8549

AN:

20198

East Asian (EAS)

AF:

0.293

AC:

10368

AN:

35406

South Asian (SAS)

AF:

0.367

AC:

22357

AN:

60972

European-Finnish (FIN)

AF:

0.394

AC:

14047

AN:

35608

Middle Eastern (MID)

AF:

0.431

AC:

1707

AN:

3960

European-Non Finnish (NFE)

AF:

0.438

AC:

406073

AN:

926384

Other (OTH)

AF:

0.420

AC:

20538

AN:

48934

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.458

Heterozygous variant carriers

15640

31281

46921

62562

78202

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

15928

31856

47784

63712

79640

<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:

0.550

AC:

75938

AN:

138014

Hom.:

20562

Cov.:

AF XY:

0.544

AC XY:

36199

AN XY:

66542

show subpopulations

African (AFR)

AF:

0.486

AC:

18481

AN:

38012

American (AMR)

AF:

0.570

AC:

7840

AN:

13760

Ashkenazi Jewish (ASJ)

AF:

0.652

AC:

2149

AN:

3294

East Asian (EAS)

AF:

0.322

AC:

1560

AN:

4840

South Asian (SAS)

AF:

0.431

AC:

1851

AN:

4290

European-Finnish (FIN)

AF:

0.524

AC:

3919

AN:

7472

Middle Eastern (MID)

AF:

0.621

AC:

154

AN:

248

European-Non Finnish (NFE)

AF:

0.606

AC:

38409

AN:

63384

Other (OTH)

AF:

0.585

AC:

1099

AN:

1880

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

1563

3127

4690

6254

7817

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

656

1312

1968

2624

3280

<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

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.27

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

12-104866587-TAAAAAAAAA-TAAAAAAAA

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