Genetic Variant NM_001352171.3:c.1175+43_1175+50dupGTGTGTGT (chr12-104866381-T-TACACACAC) – 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.1175+43_1175+50dupGTGTGTGT 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 0.00018 ( 0 hom., cov: 0)

Exomes 𝑓: 0.000013 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

SLC41A2
NM_001352171.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.602

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:

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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	HGVSp	Effect	Exon Rank	Protein	UniProt
SLC41A2	NM_001352171.3	MANE Select	c.1175+43_1175+50dupGTGTGTGT		intron	N/A	NP_001339100.1	Q96JW4
SLC41A2	NM_001387131.1		c.1218_1225dupGTGTGTGT	p.Tyr409CysfsTer21	frameshift	Exon 7 of 7	NP_001374060.1
SLC41A2	NM_001387132.1		c.1218_1225dupGTGTGTGT	p.Tyr409CysfsTer21	frameshift	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+50_1175+51insGTGTGTGT	intron	N/A	ENSP00000258538.3	Q96JW4
SLC41A2	ENST00000906846.1		c.1175+50_1175+51insGTGTGTGT	intron	N/A	ENSP00000576905.1
SLC41A2	ENST00000906847.1		c.1175+50_1175+51insGTGTGTGT	intron	N/A	ENSP00000576906.1

Frequencies

GnomAD3 genomes

AF:

0.000184

AC:

AN:

141012

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000626

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:

0.0000462

Gnomad OTH

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0000132

AC:

AN:

1286206

Hom.:

Cov.:

AF XY:

0.0000158

AC XY:

AN XY:

632070

show subpopulations

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

African (AFR)

AF:

0.000420

AC:

AN:

28578

American (AMR)

AF:

0.00

AC:

AN:

31802

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

20612

East Asian (EAS)

AF:

0.0000836

AC:

AN:

35884

South Asian (SAS)

AF:

0.0000177

AC:

AN:

56378

European-Finnish (FIN)

AF:

0.00

AC:

AN:

40944

Middle Eastern (MID)

AF:

0.00

AC:

AN:

4704

European-Non Finnish (NFE)

AF:

9.86e-7

AC:

AN:

1014706

Other (OTH)

AF:

0.00

AC:

AN:

52598

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.0000000000000334177), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.328

Heterozygous variant carriers

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

AF:

0.000184

AC:

AN:

141012

Hom.:

Cov.:

AF XY:

0.000175

AC XY:

AN XY:

68556

show subpopulations

African (AFR)

AF:

0.000626

AC:

AN:

36730

American (AMR)

AF:

0.00

AC:

AN:

14306

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3330

East Asian (EAS)

AF:

0.00

AC:

AN:

4724

South Asian (SAS)

AF:

0.00

AC:

AN:

4228

European-Finnish (FIN)

AF:

0.00

AC:

AN:

9668

Middle Eastern (MID)

AF:

0.00

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0000462

AC:

AN:

64940

Other (OTH)

AF:

0.00

AC:

AN:

1930

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.467

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.:

405

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.60

Splicing

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

Publications

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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