chr18-45663836-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_007163.4(SLC14A2):c.1403C>T(p.Ser468Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000273 in 1,613,022 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_007163.4 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 |
---|---|---|---|---|---|---|---|
SLC14A2 | NM_007163.4 | c.1403C>T | p.Ser468Leu | missense_variant | 11/20 | ENST00000255226.11 | |
LOC105372093 | XR_935423.3 | n.873-26679G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC14A2 | ENST00000255226.11 | c.1403C>T | p.Ser468Leu | missense_variant | 11/20 | 1 | NM_007163.4 | P1 | |
SLC14A2 | ENST00000586448.5 | c.1403C>T | p.Ser468Leu | missense_variant | 12/21 | 2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000145 AC: 22AN: 151924Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000598 AC: 15AN: 250862Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135606
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1460980Hom.: 0 Cov.: 31 AF XY: 0.00000688 AC XY: 5AN XY: 726840
GnomAD4 genome ? AF: 0.000145 AC: 22AN: 152042Hom.: 0 Cov.: 31 AF XY: 0.000148 AC XY: 11AN XY: 74320
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 26, 2022 | The c.1403C>T (p.S468L) alteration is located in exon 11 (coding exon 10) of the SLC14A2 gene. This alteration results from a C to T substitution at nucleotide position 1403, causing the serine (S) at amino acid position 468 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