GeneBe

rs57548373

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001387131.1(SLC41A2):​c.1204_1225delGTGTGTGTGTGTGTGTGTGTGT​(p.Val402ThrfsTer18) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000777 in 1,286,220 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)
Exomes 𝑓: 0.0000078 ( 0 hom. )

Consequence

SLC41A2
NM_001387131.1 frameshift

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.94

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]

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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_001387131.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
SLC41A2
NM_001352171.3
MANE Select
c.1175+29_1175+50delGTGTGTGTGTGTGTGTGTGTGT
intron
N/ANP_001339100.1Q96JW4
SLC41A2
NM_001387131.1
c.1204_1225delGTGTGTGTGTGTGTGTGTGTGTp.Val402ThrfsTer18
frameshift
Exon 7 of 7NP_001374060.1
SLC41A2
NM_001387132.1
c.1204_1225delGTGTGTGTGTGTGTGTGTGTGTp.Val402ThrfsTer18
frameshift
Exon 8 of 8NP_001374061.1

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
SLC41A2
ENST00000258538.8
TSL:1 MANE Select
c.1175+29_1175+50delGTGTGTGTGTGTGTGTGTGTGT
intron
N/AENSP00000258538.3Q96JW4
SLC41A2
ENST00000906846.1
c.1175+29_1175+50delGTGTGTGTGTGTGTGTGTGTGT
intron
N/AENSP00000576905.1
SLC41A2
ENST00000906847.1
c.1175+29_1175+50delGTGTGTGTGTGTGTGTGTGTGT
intron
N/AENSP00000576906.1

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
AF:
0.00000777
AC:
10
AN:
1286220
Hom.:
0
AF XY:
0.00000316
AC XY:
2
AN XY:
632072
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
28586
American (AMR)
AF:
0.00
AC:
0
AN:
31802
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
20612
East Asian (EAS)
AF:
0.00
AC:
0
AN:
35884
South Asian (SAS)
AF:
0.00
AC:
0
AN:
56380
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
40944
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
4704
European-Non Finnish (NFE)
AF:
0.00000887
AC:
9
AN:
1014708
Other (OTH)
AF:
0.0000190
AC:
1
AN:
52600
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.425
Heterozygous variant carriers
0
1
2
2
3
4
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<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
Cov.:
0
Alfa
AF:
0.00
Hom.:
405

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

Other links and lift over

dbSNP: rs57548373; hg19: chr12-105260159; API