Genetic Variant SLC41A2:c.1028-10_1028-9delTT (chr12-104866587-TAA-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.1028-10_1028-9delTT variant causes a 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 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.06

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-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 rank	MANE	Protein	UniProt
SLC41A2	NM_001352171.3 link	c.1028-10_1028-9delTT		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 link	c.1028-10_1028-9delTT		intron_variant	Intron 6 of 10	1	NM_001352171.3	ENSP00000258538.3		Q96JW4
ENSG00000286410	ENST00000671114.1 link	n.71-3574_71-3573delAA		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.167

AC:

23008

AN:

138160

Hom.:

3131

Cov.:

show subpopulations

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

GnomAD2 exomes

AF:

0.280

AC:

35111

AN:

125200

AF XY:

0.279

show subpopulations

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 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

show subpopulations

Gnomad4 AFR exome

AF:

0.415

AC:

10846

AN:

26144

Gnomad4 AMR exome

AF:

0.266

AC:

7010

AN:

26364

Gnomad4 ASJ exome

AF:

0.269

AC:

5254

AN:

19520

Gnomad4 EAS exome

AF:

0.275

AC:

9734

AN:

35456

Gnomad4 SAS exome

AF:

0.209

AC:

12636

AN:

60342

Gnomad4 FIN exome

AF:

0.237

AC:

8283

AN:

34890

Gnomad4 NFE exome

AF:

0.212

AC:

190732

AN:

898048

Gnomad4 Remaining exome

AF:

0.240

AC:

11452

AN:

47662

Heterozygous variant carriers

13298

26597

39895

53194

66492

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Exome Het

Exome Hom

Variant carriers

7212

14424

21636

28848

36060

<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:

0.167

AC:

23042

AN:

138190

Hom.:

3133

Cov.:

AF XY:

0.168

AC XY:

11197

AN XY:

66626

show subpopulations

Gnomad4 AFR

AF:

0.384

AC:

0.384163

AN:

0.384163

Gnomad4 AMR

AF:

0.113

AC:

0.112943

AN:

0.112943

Gnomad4 ASJ

AF:

0.0774

AC:

0.0773665

AN:

0.0773665

Gnomad4 EAS

AF:

0.254

AC:

0.254335

AN:

0.254335

Gnomad4 SAS

AF:

0.103

AC:

0.103497

AN:

0.103497

Gnomad4 FIN

AF:

0.111

AC:

0.111126

AN:

0.111126

Gnomad4 NFE

AF:

0.0592

AC:

0.0592427

AN:

0.0592427

Gnomad4 OTH

AF:

0.140

AC:

0.140276

AN:

0.140276

Heterozygous variant carriers

771

1543

2314

3086

3857

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Genome Het

Genome Hom

Variant carriers

228

456

684

912

1140

<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

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

May 04, 2021

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Mutation Taster

=100/0

polymorphism (auto)

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

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over