Genetic Variant SLC41A2:c.1175+45_1175+50delGTGTGT (chr12-104866381-TACACAC-T) – ACMG Classification: Benign (-11 pts)

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP3BP6_ModerateBA1

The NM_001387131.1(SLC41A2):c.1220_1225delGTGTGT(p.Cys407_Val408del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.53 ( 19420 hom., cov: 0)

Exomes 𝑓: 0.42 ( 19362 hom. )

Failed GnomAD Quality Control

Consequence

SLC41A2
NM_001387131.1 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.25

Publications

2 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

new If you want to explore the variant's impact on the transcript NM_001387131.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -11 ACMG points.

BP3

Nonframeshift variant in repetitive region in NM_001387131.1

BP6

Variant 12-104866381-TACACAC-T is Benign according to our data. Variant chr12-104866381-TACACAC-T is described in ClinVar as Benign. ClinVar VariationId is 1267960.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.596 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001387131.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
SLC41A2	NM_001352171.3	MANE Select	c.1175+45_1175+50delGTGTGT		intron	N/A	NP_001339100.1	Q96JW4
SLC41A2	NM_001387131.1		c.1220_1225delGTGTGT	p.Cys407_Val408del	disruptive_inframe_deletion	Exon 7 of 7	NP_001374060.1
SLC41A2	NM_001387132.1		c.1220_1225delGTGTGT	p.Cys407_Val408del	disruptive_inframe_deletion	Exon 8 of 8	NP_001374061.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SLC41A2	ENST00000258538.8	TSL:1 MANE Select	c.1175+45_1175+50delGTGTGT	intron	N/A	ENSP00000258538.3	Q96JW4
SLC41A2	ENST00000906846.1		c.1175+45_1175+50delGTGTGT	intron	N/A	ENSP00000576905.1
SLC41A2	ENST00000906847.1		c.1175+45_1175+50delGTGTGT	intron	N/A	ENSP00000576906.1

Frequencies

GnomAD3 genomes

AF:

0.533

AC:

75053

AN:

140758

Hom.:

19427

Cov.:

show subpopulations

Gnomad AFR

AF:

0.429

Gnomad AMI

AF:

0.579

Gnomad AMR

AF:

0.566

Gnomad ASJ

AF:

0.647

Gnomad EAS

AF:

0.346

Gnomad SAS

AF:

0.425

Gnomad FIN

AF:

0.507

Gnomad MID

AF:

0.623

Gnomad NFE

AF:

0.601

Gnomad OTH

AF:

0.575

GnomAD2 exomes

AF:

0.413

AC:

62517

AN:

151248

AF XY:

0.414

show subpopulations

Gnomad AFR exome

AF:

0.352

Gnomad AMR exome

AF:

0.430

Gnomad ASJ exome

AF:

0.474

Gnomad EAS exome

AF:

0.291

Gnomad FIN exome

AF:

0.433

Gnomad NFE exome

AF:

0.444

Gnomad OTH exome

AF:

0.437

GnomAD4 exome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.419

AC:

537454

AN:

1281648

Hom.:

19362

AF XY:

0.418

AC XY:

263224

AN XY:

629744

show subpopulations

African (AFR)

AF:

0.325

AC:

9228

AN:

28372

American (AMR)

AF:

0.408

AC:

12875

AN:

31568

Ashkenazi Jewish (ASJ)

AF:

0.450

AC:

9224

AN:

20516

East Asian (EAS)

AF:

0.317

AC:

11239

AN:

35510

South Asian (SAS)

AF:

0.340

AC:

19088

AN:

56078

European-Finnish (FIN)

AF:

0.403

AC:

16427

AN:

40760

Middle Eastern (MID)

AF:

0.457

AC:

2148

AN:

4698

European-Non Finnish (NFE)

AF:

0.430

AC:

435404

AN:

1011748

Other (OTH)

AF:

0.416

AC:

21821

AN:

52398

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.539

Heterozygous variant carriers

14518

29037

43555

58074

72592

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

17158

34316

51474

68632

85790

<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:

0.533

AC:

75073

AN:

140848

Hom.:

19420

Cov.:

AF XY:

0.528

AC XY:

36144

AN XY:

68516

show subpopulations

African (AFR)

AF:

0.429

AC:

15758

AN:

36730

American (AMR)

AF:

0.566

AC:

8083

AN:

14284

Ashkenazi Jewish (ASJ)

AF:

0.647

AC:

2150

AN:

3324

East Asian (EAS)

AF:

0.346

AC:

1627

AN:

4706

South Asian (SAS)

AF:

0.427

AC:

1797

AN:

4212

European-Finnish (FIN)

AF:

0.507

AC:

4899

AN:

9656

Middle Eastern (MID)

AF:

0.637

AC:

172

AN:

270

European-Non Finnish (NFE)

AF:

0.601

AC:

38975

AN:

64856

Other (OTH)

AF:

0.571

AC:

1112

AN:

1946

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1653

3306

4959

6612

8265

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

664

1328

1992

2656

3320

<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:

0.354

Hom.:

405

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

1.3

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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12-104866381-TACACACACACACACACACACAC-TACACACACACACACAC

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