chr5-1232278-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_182632.3(SLC6A18):c.220G>A(p.Val74Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000107 in 1,612,994 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_182632.3 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC6A18 | NM_182632.3 | c.220G>A | p.Val74Ile | missense_variant | 2/12 | ENST00000324642.4 | NP_872438.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC6A18 | ENST00000324642.4 | c.220G>A | p.Val74Ile | missense_variant | 2/12 | 1 | NM_182632.3 | ENSP00000323549.3 | ||
SLC6A18 | ENST00000513607.2 | n.289G>A | non_coding_transcript_exon_variant | 2/3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000217 AC: 33AN: 152202Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000117 AC: 29AN: 247942Hom.: 0 AF XY: 0.000126 AC XY: 17AN XY: 134536
GnomAD4 exome AF: 0.0000952 AC: 139AN: 1460674Hom.: 0 Cov.: 37 AF XY: 0.0000853 AC XY: 62AN XY: 726592
GnomAD4 genome AF: 0.000217 AC: 33AN: 152320Hom.: 0 Cov.: 34 AF XY: 0.000255 AC XY: 19AN XY: 74476
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 17, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at