ENST00000448810.6:n.-30G>C
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000448810.6(SLC22A5):n.-164A>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
SLC22A5
ENST00000448810.6 upstream_gene
ENST00000448810.6 upstream_gene
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.898
Publications
0 publications found
Genes affected
SLC22A5 (HGNC:10969): (solute carrier family 22 member 5) Polyspecific organic cation transporters in the liver, kidney, intestine, and other organs are critical for elimination of many endogenous small organic cations as well as a wide array of drugs and environmental toxins. The encoded protein is a plasma integral membrane protein which functions both as an organic cation transporter and as a sodium-dependent high affinity carnitine transporter. The encoded protein is involved in the active cellular uptake of carnitine. Mutations in this gene are the cause of systemic primary carnitine deficiency (CDSP), an autosomal recessive disorder manifested early in life by hypoketotic hypoglycemia and acute metabolic decompensation, and later in life by skeletal myopathy or cardiomyopathy. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Apr 2015]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 711484Hom.: 0 Cov.: 9 AF XY: 0.00 AC XY: 0AN XY: 361432
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
711484
Hom.:
Cov.:
9
AF XY:
AC XY:
0
AN XY:
361432
African (AFR)
AF:
AC:
0
AN:
13916
American (AMR)
AF:
AC:
0
AN:
15572
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
14308
East Asian (EAS)
AF:
AC:
0
AN:
29566
South Asian (SAS)
AF:
AC:
0
AN:
48782
European-Finnish (FIN)
AF:
AC:
0
AN:
30108
Middle Eastern (MID)
AF:
AC:
0
AN:
2466
European-Non Finnish (NFE)
AF:
AC:
0
AN:
522628
Other (OTH)
AF:
AC:
0
AN:
34138
GnomAD4 genome Cov.: 33
GnomAD4 genome
Cov.:
33
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
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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