rs121918238
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_001177316.2(SLC34A3):c.1402C>A(p.Arg468=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000147 in 1,612,510 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. R468R) has been classified as Likely benign.
Frequency
Consequence
NM_001177316.2 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC34A3 | NM_001177316.2 | c.1402C>A | p.Arg468= | synonymous_variant | 13/13 | ENST00000673835.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC34A3 | ENST00000673835.1 | c.1402C>A | p.Arg468= | synonymous_variant | 13/13 | NM_001177316.2 | P1 | ||
SLC34A3 | ENST00000361134.2 | c.1402C>A | p.Arg468= | synonymous_variant | 13/13 | 2 | P1 | ||
SLC34A3 | ENST00000538474.5 | c.1402C>A | p.Arg468= | synonymous_variant | 13/13 | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152242Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000567 AC: 14AN: 246806Hom.: 0 AF XY: 0.0000446 AC XY: 6AN XY: 134482
GnomAD4 exome AF: 0.000158 AC: 230AN: 1460268Hom.: 0 Cov.: 31 AF XY: 0.000165 AC XY: 120AN XY: 726438
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152242Hom.: 0 Cov.: 34 AF XY: 0.0000134 AC XY: 1AN XY: 74384
ClinVar
Submissions by phenotype
Autosomal recessive hypophosphatemic bone disease Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Aug 12, 2021 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 05, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at