Genetic Variant SLC41A2:c.1028-13_1028-9delTTTTT (chr12-104866587-TAAAAA-T) – 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.1028-13_1028-9delTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000182 in 1,201,052 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0 ( 0 hom., cov: 0)

Exomes 𝑓: 0.00018 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

SLC41A2
NM_001352171.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.94

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.1028-13_1028-9delTTTTT	intron	N/A	NP_001339100.1	Q96JW4
SLC41A2	NM_001352169.2		c.1028-13_1028-9delTTTTT	intron	N/A	NP_001339098.1	Q96JW4
SLC41A2	NM_001352170.3		c.1028-13_1028-9delTTTTT	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.1028-13_1028-9delTTTTT	intron	N/A	ENSP00000258538.3	Q96JW4
SLC41A2	ENST00000906846.1		c.1028-13_1028-9delTTTTT	intron	N/A	ENSP00000576905.1
SLC41A2	ENST00000906847.1		c.1028-13_1028-9delTTTTT	intron	N/A	ENSP00000576906.1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

138222

Hom.:

Cov.:

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.000455

AC:

AN:

125200

AF XY:

0.000389

show subpopulations

Gnomad AFR exome

AF:

0.000218

Gnomad AMR exome

AF:

0.000900

Gnomad ASJ exome

AF:

0.000413

Gnomad EAS exome

AF:

0.00134

Gnomad FIN exome

AF:

0.000623

Gnomad NFE exome

AF:

0.000281

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.000182

AC:

218

AN:

1201052

Hom.:

AF XY:

0.000204

AC XY:

122

AN XY:

597514

show subpopulations

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

African (AFR)

AF:

0.000299

AC:

AN:

26742

American (AMR)

AF:

0.000628

AC:

AN:

27082

Ashkenazi Jewish (ASJ)

AF:

0.000294

AC:

AN:

20386

East Asian (EAS)

AF:

0.000800

AC:

AN:

36256

South Asian (SAS)

AF:

0.000291

AC:

AN:

61916

European-Finnish (FIN)

AF:

0.000638

AC:

AN:

36034

Middle Eastern (MID)

AF:

0.000249

AC:

AN:

4016

European-Non Finnish (NFE)

AF:

0.000106

AC:

100

AN:

938990

Other (OTH)

AF:

0.000322

AC:

AN:

49630

⚠️ 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: 0.253

Heterozygous variant carriers

120

150

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome 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

GnomAD4 genome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

138222

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

66600

African (AFR)

AF:

0.00

AC:

AN:

38052

American (AMR)

AF:

0.00

AC:

AN:

13768

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3296

East Asian (EAS)

AF:

0.00

AC:

AN:

4862

South Asian (SAS)

AF:

0.00

AC:

AN:

4318

European-Finnish (FIN)

AF:

0.00

AC:

AN:

7480

Middle Eastern (MID)

AF:

0.00

AC:

AN:

274

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

63470

Other (OTH)

AF:

0.00

AC:

AN:

1866

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

1.9

Splicing

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

Publications

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12-104866587-TAAAAAAAAA-TAAAA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over