NM_144585.4:c.51G>A
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_144585.4(SLC22A12):c.51G>A(p.Gln17Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,613,208 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
SLC22A12
NM_144585.4 synonymous
NM_144585.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.82
Publications
2 publications found
Genes affected
SLC22A12 (HGNC:17989): (solute carrier family 22 member 12) The protein encoded by this gene is a member of the organic anion transporter (OAT) family, and it acts as a urate transporter to regulate urate levels in blood. This protein is an integral membrane protein primarily found in epithelial cells of the proximal tubule of the kidney. An elevated level of serum urate, hyperuricemia, is associated with increased incidences of gout, and mutations in this gene cause renal hypouricemia type 1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2013]
SLC22A12 Gene-Disease associations (from GenCC):
- hypouricemia, renal 1Inheritance: AR Classification: STRONG Submitted by: PanelApp Australia, Labcorp Genetics (formerly Invitae)
- hereditary renal hypouricemiaInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.5).
BP7
Synonymous conserved (PhyloP=1.82 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_144585.4. 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 |
|---|---|---|---|---|---|---|---|---|---|
| SLC22A12 | NM_144585.4 | MANE Select | c.51G>A | p.Gln17Gln | synonymous | Exon 1 of 10 | NP_653186.2 | ||
| SLC22A12 | NM_001276326.2 | c.51G>A | p.Gln17Gln | synonymous | Exon 1 of 10 | NP_001263255.1 | Q96S37-4 | ||
| SLC22A12 | NM_001276327.2 | c.51G>A | p.Gln17Gln | synonymous | Exon 1 of 8 | NP_001263256.1 | Q96S37-2 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| SLC22A12 | ENST00000377574.6 | TSL:1 MANE Select | c.51G>A | p.Gln17Gln | synonymous | Exon 1 of 10 | ENSP00000366797.1 | Q96S37-1 | |
| SLC22A12 | ENST00000336464.7 | TSL:1 | c.51G>A | p.Gln17Gln | synonymous | Exon 1 of 10 | ENSP00000336836.7 | Q96S37-4 | |
| SLC22A12 | ENST00000377572.5 | TSL:1 | c.51G>A | p.Gln17Gln | synonymous | Exon 1 of 8 | ENSP00000366795.1 | Q96S37-2 |
Frequencies
GnomAD3 genomes 0.00000657 AC: 1AN: 152200Hom.: 0 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
152200
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
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Gnomad ASJ
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Gnomad EAS
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Gnomad SAS
AF:
Gnomad FIN
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Gnomad MID
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Gnomad NFE
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Gnomad OTH
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GnomAD2 exomes AF: 0.00000399 AC: 1AN: 250562 AF XY: 0.00 show subpopulations
GnomAD2 exomes
AF:
AC:
1
AN:
250562
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
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Gnomad ASJ exome
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Gnomad EAS exome
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Gnomad FIN exome
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Gnomad NFE exome
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Gnomad OTH exome
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GnomAD4 exome AF: 0.00000137 AC: 2AN: 1460890Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 726768 show subpopulations
GnomAD4 exome
AF:
AC:
2
AN:
1460890
Hom.:
Cov.:
30
AF XY:
AC XY:
1
AN XY:
726768
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33480
American (AMR)
AF:
AC:
0
AN:
44724
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26134
East Asian (EAS)
AF:
AC:
0
AN:
39700
South Asian (SAS)
AF:
AC:
0
AN:
86258
European-Finnish (FIN)
AF:
AC:
0
AN:
52428
Middle Eastern (MID)
AF:
AC:
0
AN:
5768
European-Non Finnish (NFE)
AF:
AC:
2
AN:
1112008
Other (OTH)
AF:
AC:
0
AN:
60390
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome 0.00000657 AC: 1AN: 152318Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74496 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
152318
Hom.:
Cov.:
33
AF XY:
AC XY:
0
AN XY:
74496
show subpopulations
African (AFR)
AF:
AC:
0
AN:
41570
American (AMR)
AF:
AC:
0
AN:
15302
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3472
East Asian (EAS)
AF:
AC:
1
AN:
5186
South Asian (SAS)
AF:
AC:
0
AN:
4824
European-Finnish (FIN)
AF:
AC:
0
AN:
10628
Middle Eastern (MID)
AF:
AC:
0
AN:
294
European-Non Finnish (NFE)
AF:
AC:
0
AN:
68016
Other (OTH)
AF:
AC:
0
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.675
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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