rs35526408
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001099646.3(SLC47A2):c.1572C>T(p.His524=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000794 in 1,614,120 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00060 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00081 ( 6 hom. )
Consequence
SLC47A2
NM_001099646.3 synonymous
NM_001099646.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.56
Genes affected
SLC47A2 (HGNC:26439): (solute carrier family 47 member 2) This gene encodes a protein belonging to a family of transporters involved in excretion of toxic electrolytes, both endogenous and exogenous, through urine and bile. This transporter family shares homology with the bacterial MATE (multidrug and toxin extrusion) protein family responsible for drug resistance. This gene is one of two members of the MATE transporter family located near each other on chromosome 17. Alternatively spliced transcript variants encoding different isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]
ALDH3A2 (HGNC:403): (aldehyde dehydrogenase 3 family member A2) Aldehyde dehydrogenase isozymes are thought to play a major role in the detoxification of aldehydes generated by alcohol metabolism and lipid peroxidation. This gene product catalyzes the oxidation of long-chain aliphatic aldehydes to fatty acid. Mutations in the gene cause Sjogren-Larsson syndrome. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
?
Variant 17-19678815-G-A is Benign according to our data. Variant chr17-19678815-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2647563.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-3.56 with no splicing effect.
BS2
?
High Homozygotes in GnomAdExome4 at 6 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC47A2 | NM_001099646.3 | c.1572C>T | p.His524= | synonymous_variant | 17/17 | ENST00000433844.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC47A2 | ENST00000433844.4 | c.1572C>T | p.His524= | synonymous_variant | 17/17 | 5 | NM_001099646.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000598 AC: 91AN: 152230Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000702 AC: 176AN: 250728Hom.: 0 AF XY: 0.000760 AC XY: 103AN XY: 135596
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GnomAD4 exome AF: 0.000814 AC: 1190AN: 1461772Hom.: 6 Cov.: 30 AF XY: 0.000806 AC XY: 586AN XY: 727178
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GnomAD4 genome ? AF: 0.000597 AC: 91AN: 152348Hom.: 0 Cov.: 32 AF XY: 0.000577 AC XY: 43AN XY: 74504
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Sep 01, 2022 | SLC47A2: BP4, BP7 - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at