12-128823531-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_145648.4(SLC15A4):āc.413T>Cā(p.Leu138Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000231 in 1,469,120 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 (ā ).
Frequency
Consequence
NM_145648.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC15A4 | NM_145648.4 | c.413T>C | p.Leu138Pro | missense_variant | 1/8 | ENST00000266771.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC15A4 | ENST00000266771.10 | c.413T>C | p.Leu138Pro | missense_variant | 1/8 | 1 | NM_145648.4 | P1 | |
SLC15A4 | ENST00000539703.1 | n.63T>C | non_coding_transcript_exon_variant | 1/4 | 5 | ||||
SLC15A4 | ENST00000376744.8 | c.251T>C | p.Leu84Pro | missense_variant, NMD_transcript_variant | 1/7 | 2 | |||
SLC15A4 | ENST00000376740.8 | upstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152046Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000139 AC: 1AN: 71946Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 41782
GnomAD4 exome AF: 0.0000114 AC: 15AN: 1316966Hom.: 0 Cov.: 31 AF XY: 0.00000924 AC XY: 6AN XY: 649332
GnomAD4 genome AF: 0.000125 AC: 19AN: 152154Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 74406
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 04, 2023 | The c.413T>C (p.L138P) alteration is located in exon 1 (coding exon 1) of the SLC15A4 gene. This alteration results from a T to C substitution at nucleotide position 413, causing the leucine (L) at amino acid position 138 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at