rs142901935
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_001010898.4(SLC6A17):c.525G>A(p.Pro175=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000288 in 1,614,132 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00019 ( 1 hom. )
Consequence
SLC6A17
NM_001010898.4 synonymous
NM_001010898.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.11
Genes affected
SLC6A17 (HGNC:31399): (solute carrier family 6 member 17) The protein encoded by this gene is a member of the SLC6 family of transporters, which are responsible for the presynaptic uptake of most neurotransmitters. The encoded vesicular transporter is selective for proline, glycine, leucine and alanine. In mouse, the strongest expression of this gene was in cortical and hippocampal tissues where expression increased during embryonic brain development and peaked postnatally. Defects in this gene cause a form of autosomal recessive intellectual disability. [provided by RefSeq, Jul 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
Variant 1-110174053-G-A is Benign according to our data. Variant chr1-110174053-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 436762.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-3.11 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC6A17 | NM_001010898.4 | c.525G>A | p.Pro175= | synonymous_variant | 4/12 | ENST00000331565.5 | NP_001010898.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC6A17 | ENST00000331565.5 | c.525G>A | p.Pro175= | synonymous_variant | 4/12 | 2 | NM_001010898.4 | ENSP00000330199 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00127 AC: 193AN: 152178Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000338 AC: 85AN: 251434Hom.: 0 AF XY: 0.000235 AC XY: 32AN XY: 135890
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GnomAD4 exome AF: 0.000185 AC: 271AN: 1461836Hom.: 1 Cov.: 31 AF XY: 0.000160 AC XY: 116AN XY: 727214
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GnomAD4 genome AF: 0.00127 AC: 194AN: 152296Hom.: 0 Cov.: 32 AF XY: 0.00134 AC XY: 100AN XY: 74478
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 31, 2019 | - - |
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jan 19, 2017 | - - |
Progressive essential tremor-speech impairment-facial dysmorphism-intellectual disability-abnormal behavior syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Apr 11, 2023 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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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