12-128799328-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_145648.4(SLC15A4):c.1504G>T(p.Val502Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000217 in 1,614,006 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V502M) has been classified as Uncertain significance.
Frequency
Consequence
NM_145648.4 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 | UniProt |
---|---|---|---|---|---|---|---|
SLC15A4 | NM_145648.4 | c.1504G>T | p.Val502Leu | missense_variant | 7/8 | ENST00000266771.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC15A4 | ENST00000266771.10 | c.1504G>T | p.Val502Leu | missense_variant | 7/8 | 1 | NM_145648.4 | P1 | |
SLC15A4 | ENST00000544112.5 | n.1378G>T | non_coding_transcript_exon_variant | 4/5 | 2 | ||||
SLC15A4 | ENST00000545031.5 | n.938G>T | non_coding_transcript_exon_variant | 2/3 | 2 | ||||
SLC15A4 | ENST00000376744.8 | c.*456G>T | 3_prime_UTR_variant, NMD_transcript_variant | 6/7 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152116Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251486Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135920
GnomAD4 exome AF: 0.0000233 AC: 34AN: 1461890Hom.: 0 Cov.: 31 AF XY: 0.0000275 AC XY: 20AN XY: 727248
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152116Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74296
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 08, 2023 | The c.1504G>T (p.V502L) alteration is located in exon 7 (coding exon 7) of the SLC15A4 gene. This alteration results from a G to T substitution at nucleotide position 1504, causing the valine (V) at amino acid position 502 to be replaced by a leucine (L). 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