3-45755459-C-T
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_020208.4(SLC6A20):c.*3519G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 152,136 control chromosomes in the GnomAD database, including 11,036 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.35 ( 11031 hom., cov: 33)
Exomes 𝑓: 0.50 ( 5 hom. )
Consequence
SLC6A20
NM_020208.4 3_prime_UTR
NM_020208.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.508
Genes affected
SLC6A20 (HGNC:30927): (solute carrier family 6 member 20) Transport of small hydrophilic substances across cell membranes is mediated by substrate-specific transporter proteins which have been classified into several families of related genes. The protein encoded by this gene belongs to the sodium:neurotransmitter symporter (SNF) family and functions as a proline transporter expressed in kidney and small intestine. Mutations in this gene are associated with Hyperglycinuria and Iminoglycinuria. [provided by RefSeq, Jul 2020]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BP6
Variant 3-45755459-C-T is Benign according to our data. Variant chr3-45755459-C-T is described in ClinVar as [Benign]. Clinvar id is 345340.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC6A20 | NM_020208.4 | c.*3519G>A | 3_prime_UTR_variant | 11/11 | ENST00000358525.9 | NP_064593.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC6A20 | ENST00000358525.9 | c.*3519G>A | 3_prime_UTR_variant | 11/11 | 1 | NM_020208.4 | ENSP00000346298.4 | |||
SLC6A20 | ENST00000353278.8 | c.*3519G>A | 3_prime_UTR_variant | 10/10 | 1 | ENSP00000296133.5 |
Frequencies
GnomAD3 genomes AF: 0.348 AC: 52957AN: 151984Hom.: 11032 Cov.: 33
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GnomAD4 exome AF: 0.500 AC: 17AN: 34Hom.: 5 Cov.: 0 AF XY: 0.500 AC XY: 8AN XY: 16
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GnomAD4 genome AF: 0.348 AC: 52972AN: 152102Hom.: 11031 Cov.: 33 AF XY: 0.347 AC XY: 25827AN XY: 74380
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Hyperglycinuria Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at