chr5-1235629-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_182632.3(SLC6A18):c.588G>A(p.Met196Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00717 in 1,613,974 control chromosomes in the GnomAD database, including 38 homozygotes. 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 Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC6A18 | NM_182632.3 | c.588G>A | p.Met196Ile | missense_variant | 4/12 | ENST00000324642.4 | NP_872438.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC6A18 | ENST00000324642.4 | c.588G>A | p.Met196Ile | missense_variant | 4/12 | 1 | NM_182632.3 | ENSP00000323549.3 |
Frequencies
GnomAD3 genomes AF: 0.00514 AC: 783AN: 152190Hom.: 3 Cov.: 33
GnomAD3 exomes AF: 0.00506 AC: 1271AN: 251320Hom.: 4 AF XY: 0.00511 AC XY: 694AN XY: 135836
GnomAD4 exome AF: 0.00738 AC: 10785AN: 1461666Hom.: 35 Cov.: 31 AF XY: 0.00714 AC XY: 5193AN XY: 727126
GnomAD4 genome AF: 0.00514 AC: 783AN: 152308Hom.: 3 Cov.: 33 AF XY: 0.00534 AC XY: 398AN XY: 74476
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2022 | SLC6A18: BP4, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at