rs28407527
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_001177316.2(SLC34A3):āc.757T>Cā(p.Leu253=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 1,610,930 control chromosomes in the GnomAD database, including 151,484 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_001177316.2 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC34A3 | NM_001177316.2 | c.757T>C | p.Leu253= | splice_region_variant, synonymous_variant | 8/13 | ENST00000673835.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC34A3 | ENST00000673835.1 | c.757T>C | p.Leu253= | splice_region_variant, synonymous_variant | 8/13 | NM_001177316.2 | P1 | ||
SLC34A3 | ENST00000361134.2 | c.757T>C | p.Leu253= | splice_region_variant, synonymous_variant | 8/13 | 2 | P1 | ||
SLC34A3 | ENST00000538474.5 | c.757T>C | p.Leu253= | splice_region_variant, synonymous_variant | 8/13 | 5 | P1 | ||
SLC34A3 | ENST00000673865.1 | c.757T>C | p.Leu253= | splice_region_variant, synonymous_variant | 8/10 |
Frequencies
GnomAD3 genomes ? AF: 0.428 AC: 64956AN: 151728Hom.: 14173 Cov.: 32
GnomAD3 exomes AF: 0.451 AC: 113088AN: 250510Hom.: 26453 AF XY: 0.447 AC XY: 60739AN XY: 135748
GnomAD4 exome AF: 0.431 AC: 628292AN: 1459084Hom.: 137306 Cov.: 44 AF XY: 0.431 AC XY: 312768AN XY: 725978
GnomAD4 genome ? AF: 0.428 AC: 64987AN: 151846Hom.: 14178 Cov.: 32 AF XY: 0.433 AC XY: 32124AN XY: 74202
ClinVar
Submissions by phenotype
not provided Benign:4
Benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 17, 2018 | This variant is associated with the following publications: (PMID: 20074341) - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Jun 14, 2016 | Variant summary: SLC34A3 c.757T>C (p.Leu253=) is a synonymous change that involves a non-conserved nucleotide at the Intron 7-Exon 8 boundary. One in silico tool predicts a benign outcome, and 5/5 splicing algorithms predict that this variant does not affect normal splicing, however no functional studies supporting these in silico predictions were published at the time of evaluation. This variant was found in 53912/121368 control chromosomes (12221 homozygotes) at a frequency of 0.4442028, which is approximately 251 times the estimated maximal expected allele frequency of a pathogenic SLC34A3 variant (0.0017678), suggesting this variant is likely a benign polymorphism. Additionally, the variant of interest was classified as Benign by one clinical laboratory. Taken together, the variant was classified as Benign. Taken together, the variant was classified as Benign based on the prevalence in the general population. - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
not specified Benign:3
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jul 01, 2015 | - - |
Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Autosomal recessive hypophosphatemic bone disease Benign:1
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at