rs16928737
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The ENST00000373189.6(SLC29A3):c.597G>A(p.Gln199=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00663 in 1,612,488 control chromosomes in the GnomAD database, including 517 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.033 ( 269 hom., cov: 32)
Exomes 𝑓: 0.0039 ( 248 hom. )
Consequence
SLC29A3
ENST00000373189.6 synonymous
ENST00000373189.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.58
Genes affected
SLC29A3 (HGNC:23096): (solute carrier family 29 member 3) This gene encodes a nucleoside transporter. The encoded protein plays a role in cellular uptake of nucleosides, nucleobases, and their related analogs. Mutations in this gene have been associated with H syndrome, which is characterized by cutaneous hyperpigmentation and hypertrichosis, hepatosplenomegaly, heart anomalies, and hypogonadism. A related disorder, PHID (pigmented hypertrichosis with insulin-dependent diabetes mellitus), has also been associated with mutations at this locus. Alternatively spliced transcript variants have been described.[provided by RefSeq, Mar 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.5).
BP6
Variant 10-71351775-G-A is Benign according to our data. Variant chr10-71351775-G-A is described in ClinVar as [Benign]. Clinvar id is 130336.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-71351775-G-A is described in Lovd as [Benign].
BP7
Synonymous conserved (PhyloP=2.58 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC29A3 | NM_018344.6 | c.597G>A | p.Gln199= | synonymous_variant | 4/6 | ENST00000373189.6 | NP_060814.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC29A3 | ENST00000373189.6 | c.597G>A | p.Gln199= | synonymous_variant | 4/6 | 1 | NM_018344.6 | ENSP00000362285 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0328 AC: 4991AN: 152124Hom.: 269 Cov.: 32
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GnomAD3 exomes AF: 0.00937 AC: 2333AN: 248864Hom.: 114 AF XY: 0.00708 AC XY: 954AN XY: 134658
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GnomAD4 exome AF: 0.00390 AC: 5692AN: 1460246Hom.: 248 Cov.: 35 AF XY: 0.00349 AC XY: 2534AN XY: 726380
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GnomAD4 genome AF: 0.0328 AC: 4995AN: 152242Hom.: 269 Cov.: 32 AF XY: 0.0311 AC XY: 2313AN XY: 74438
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
H syndrome Benign:2
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. - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Mar 05, 2013 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
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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