14-23346884-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_016609.7(SLC22A17):c.1660G>A(p.Gly554Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000267 in 1,538,226 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar 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.1660G>A | p.Gly554Ser | missense_variant | 10/10 | ENST00000354772.10 | |
SLC22A17 | NM_020372.4 | c.1714G>A | p.Gly572Ser | missense_variant | 10/10 | ||
SLC22A17 | NM_001289050.1 | c.673G>A | p.Gly225Ser | missense_variant | 9/9 | ||
SLC22A17 | NR_110290.2 | n.1471G>A | non_coding_transcript_exon_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC22A17 | ENST00000354772.10 | c.1660G>A | p.Gly554Ser | missense_variant | 10/10 | 1 | NM_016609.7 | A2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152192Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000295 AC: 4AN: 135786Hom.: 0 AF XY: 0.0000404 AC XY: 3AN XY: 74224
GnomAD4 exome AF: 0.0000289 AC: 40AN: 1386034Hom.: 0 Cov.: 31 AF XY: 0.0000321 AC XY: 22AN XY: 684434
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152192Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74340
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 06, 2024 | The c.1381G>A (p.G461S) alteration is located in exon 9 (coding exon 9) of the SLC22A17 gene. This alteration results from a G to A substitution at nucleotide position 1381, causing the glycine (G) at amino acid position 461 to be replaced by a serine (S). 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