5-177385787-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003052.5(SLC34A1):c.46C>T(p.Leu16Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000821 in 1,461,072 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003052.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC34A1 | NM_003052.5 | c.46C>T | p.Leu16Phe | missense_variant | 2/13 | ENST00000324417.6 | NP_003043.3 | |
SLC34A1 | NM_001167579.2 | c.46C>T | p.Leu16Phe | missense_variant | 2/9 | NP_001161051.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC34A1 | ENST00000324417.6 | c.46C>T | p.Leu16Phe | missense_variant | 2/13 | 1 | NM_003052.5 | ENSP00000321424.4 | ||
SLC34A1 | ENST00000512593.5 | c.46C>T | p.Leu16Phe | missense_variant | 2/9 | 2 | ENSP00000423022.1 | |||
SLC34A1 | ENST00000504577.5 | c.46C>T | p.Leu16Phe | missense_variant | 2/4 | 4 | ENSP00000423733.1 | |||
SLC34A1 | ENST00000507685.5 | n.130C>T | non_coding_transcript_exon_variant | 2/10 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000122 AC: 3AN: 246456Hom.: 0 AF XY: 0.0000150 AC XY: 2AN XY: 133452
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461072Hom.: 0 Cov.: 32 AF XY: 0.0000110 AC XY: 8AN XY: 726776
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Mar 29, 2022 | Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. This variant has not been reported in the literature in individuals affected with SLC34A1-related conditions. This variant is present in population databases (rs762446018, gnomAD 0.003%). This sequence change replaces leucine, which is neutral and non-polar, with phenylalanine, which is neutral and non-polar, at codon 16 of the SLC34A1 protein (p.Leu16Phe). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at