14-23347132-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_016609.7(SLC22A17):c.1576C>T(p.Leu526Phe) variant causes a missense change. The variant allele was found at a frequency of 0.00000137 in 1,461,518 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. L526I) has been classified as Uncertain significance.
Frequency
Consequence
NM_016609.7 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 |
---|---|---|---|---|---|---|---|
SLC22A17 | NM_016609.7 | c.1576C>T | p.Leu526Phe | missense_variant | 9/10 | ENST00000354772.10 | |
SLC22A17 | NM_020372.4 | c.1630C>T | p.Leu544Phe | missense_variant | 9/10 | ||
SLC22A17 | NM_001289050.1 | c.589C>T | p.Leu197Phe | missense_variant | 8/9 | ||
SLC22A17 | NR_110290.2 | n.1387C>T | non_coding_transcript_exon_variant | 7/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC22A17 | ENST00000354772.10 | c.1576C>T | p.Leu526Phe | missense_variant | 9/10 | 1 | NM_016609.7 | A2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249106Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135058
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461518Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 727048
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 15, 2023 | The c.1297C>T (p.L433F) alteration is located in exon 8 (coding exon 8) of the SLC22A17 gene. This alteration results from a C to T substitution at nucleotide position 1297, causing the leucine (L) at amino acid position 433 to be replaced by a phenylalanine (F). 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