5-1201643-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001003841.3(SLC6A19):c.-8C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0107 in 1,603,324 control chromosomes in the GnomAD database, including 1,589 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001003841.3 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC6A19 | ENST00000304460 | c.-8C>T | 5_prime_UTR_variant | Exon 1 of 12 | 1 | NM_001003841.3 | ENSP00000305302.10 | |||
SLC6A19 | ENST00000515652.5 | n.-8C>T | non_coding_transcript_exon_variant | Exon 1 of 11 | 2 | ENSP00000425701.1 | ||||
SLC6A19 | ENST00000515652.5 | n.-8C>T | 5_prime_UTR_variant | Exon 1 of 11 | 2 | ENSP00000425701.1 |
Frequencies
GnomAD3 genomes AF: 0.0570 AC: 8675AN: 152150Hom.: 825 Cov.: 34
GnomAD3 exomes AF: 0.0144 AC: 3396AN: 235798Hom.: 327 AF XY: 0.0105 AC XY: 1356AN XY: 129140
GnomAD4 exome AF: 0.00586 AC: 8507AN: 1451056Hom.: 762 Cov.: 31 AF XY: 0.00507 AC XY: 3659AN XY: 721960
GnomAD4 genome AF: 0.0571 AC: 8695AN: 152268Hom.: 827 Cov.: 34 AF XY: 0.0543 AC XY: 4043AN XY: 74452
ClinVar
Submissions by phenotype
not provided Benign:2
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SLC6A19-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at