rs34984157
Your query was ambiguous. Multiple possible variants found:
- chr12-104866587-TAAAAAAAAA-T
- chr12-104866587-TAAAAAAAAA-TAAA
- chr12-104866587-TAAAAAAAAA-TAAAA
- chr12-104866587-TAAAAAAAAA-TAAAAA
- chr12-104866587-TAAAAAAAAA-TAAAAAA
- chr12-104866587-TAAAAAAAAA-TAAAAAAA
- chr12-104866587-TAAAAAAAAA-TAAAAAAAA
- chr12-104866587-TAAAAAAAAA-TAAAAAAAAAA
- chr12-104866587-TAAAAAAAAA-TAAAAAAAAAAA
- chr12-104866587-TAAAAAAAAA-TAAAAAAAAAAAA
- chr12-104866587-TAAAAAAAAA-TAAAAAAAAAAAAA
- chr12-104866587-TAAAAAAAAA-TAAAAAAAAAAAAAA
- chr12-104866587-TAAAAAAAAA-TAAAAAAAAAAAAAAA
- chr12-104866587-TAAAAAAAAA-TAAAAAAAAAAAAAAAA
- chr12-104866587-TAAAAAAAAA-TAAAAAAAAAAAAAAAAA
- chr12-104866587-TAAAAAAAAA-TAAAAAAAAAAAAAAAAAAAAA
- chr12-104866587-TAAAAAAAAA-TAAAAAAAAAAAAAAAAAAAAAAAAA
- chr12-104866587-TAAAAAAAAA-TAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_001352171.3(SLC41A2):c.1028-17_1028-9delTTTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000299 in 1,340,024 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 0.0000072 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0000025 ( 0 hom. )
Consequence
SLC41A2
NM_001352171.3 intron
NM_001352171.3 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.01
Publications
1 publications found
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 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
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
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| SLC41A2 | MANE Select | c.1028-17_1028-9delTTTTTTTTT | intron | N/A | NP_001339100.1 | Q96JW4 | |||
| SLC41A2 | c.1028-17_1028-9delTTTTTTTTT | intron | N/A | NP_001339098.1 | Q96JW4 | ||||
| SLC41A2 | c.1028-17_1028-9delTTTTTTTTT | intron | N/A | NP_001339099.1 | Q96JW4 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| SLC41A2 | TSL:1 MANE Select | c.1028-17_1028-9delTTTTTTTTT | intron | N/A | ENSP00000258538.3 | Q96JW4 | |||
| SLC41A2 | c.1028-17_1028-9delTTTTTTTTT | intron | N/A | ENSP00000576905.1 | |||||
| SLC41A2 | c.1028-17_1028-9delTTTTTTTTT | intron | N/A | ENSP00000576906.1 |
Frequencies
GnomAD3 genomes 0.00000723 AC: 1AN: 138224Hom.: 0 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
138224
Hom.:
Cov.:
0
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.00000250 AC: 3AN: 1201800Hom.: 0 AF XY: 0.00000335 AC XY: 2AN XY: 597884 show subpopulations
GnomAD4 exome
AF:
AC:
3
AN:
1201800
Hom.:
AF XY:
AC XY:
2
AN XY:
597884
show subpopulations
African (AFR)
AF:
AC:
0
AN:
26800
American (AMR)
AF:
AC:
0
AN:
27106
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
20394
East Asian (EAS)
AF:
AC:
0
AN:
36362
South Asian (SAS)
AF:
AC:
0
AN:
61968
European-Finnish (FIN)
AF:
AC:
0
AN:
36060
Middle Eastern (MID)
AF:
AC:
0
AN:
4018
European-Non Finnish (NFE)
AF:
AC:
3
AN:
939428
Other (OTH)
AF:
AC:
0
AN:
49664
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.592
Heterozygous variant carriers
0
0
1
1
2
2
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 0.00000723 AC: 1AN: 138224Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 66602 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
138224
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
66602
show subpopulations
African (AFR)
AF:
AC:
0
AN:
38052
American (AMR)
AF:
AC:
0
AN:
13770
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3296
East Asian (EAS)
AF:
AC:
0
AN:
4862
South Asian (SAS)
AF:
AC:
0
AN:
4318
European-Finnish (FIN)
AF:
AC:
0
AN:
7480
Middle Eastern (MID)
AF:
AC:
0
AN:
274
European-Non Finnish (NFE)
AF:
AC:
1
AN:
63470
Other (OTH)
AF:
AC:
0
AN:
1866
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome 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
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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