5-177386432-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_003052.5(SLC34A1):c.398C>T(p.Ala133Val) variant causes a missense change. The variant allele was found at a frequency of 0.00403 in 1,614,190 control chromosomes in the GnomAD database, including 23 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A133T) has been classified as Likely benign.
Frequency
Consequence
NM_003052.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC34A1 | NM_003052.5 | c.398C>T | p.Ala133Val | missense_variant | 5/13 | ENST00000324417.6 | |
SLC34A1 | NM_001167579.2 | c.398C>T | p.Ala133Val | missense_variant | 5/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC34A1 | ENST00000324417.6 | c.398C>T | p.Ala133Val | missense_variant | 5/13 | 1 | NM_003052.5 | P1 | |
SLC34A1 | ENST00000512593.5 | c.398C>T | p.Ala133Val | missense_variant | 5/9 | 2 | |||
SLC34A1 | ENST00000507685.5 | n.482C>T | non_coding_transcript_exon_variant | 5/10 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00300 AC: 456AN: 152202Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00372 AC: 936AN: 251438Hom.: 2 AF XY: 0.00389 AC XY: 528AN XY: 135904
GnomAD4 exome AF: 0.00414 AC: 6046AN: 1461870Hom.: 21 Cov.: 34 AF XY: 0.00426 AC XY: 3095AN XY: 727240
GnomAD4 genome AF: 0.00299 AC: 455AN: 152320Hom.: 2 Cov.: 32 AF XY: 0.00306 AC XY: 228AN XY: 74482
ClinVar
Submissions by phenotype
not provided Benign:3
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 22, 2021 | In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 16688119, 30778725, 31188746, 28893421, 26787776) - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2023 | SLC34A1: BS2 - |
Nephrocalcinosis Pathogenic:1
Likely pathogenic, no assertion criteria provided | literature only | Yale Center for Mendelian Genomics, Yale University | Sep 08, 2017 | - - |
Hypophosphatemic nephrolithiasis/osteoporosis 1;C3150652:Fanconi renotubular syndrome 2;C4310473:Hypercalcemia, infantile, 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Apr 15, 2022 | - - |
Hypophosphatemic nephrolithiasis/osteoporosis 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. - |
SLC34A1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 13, 2020 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at