5-132294607-A-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_003059.3(SLC22A4):c.-10A>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000407 in 1,614,162 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_003059.3 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC22A4 | ENST00000200652 | c.-10A>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 10 | 1 | NM_003059.3 | ENSP00000200652.3 | |||
SLC22A4 | ENST00000200652 | c.-10A>T | 5_prime_UTR_variant | Exon 1 of 10 | 1 | NM_003059.3 | ENSP00000200652.3 | |||
P4HA2 | ENST00000471826.1 | n.138+571T>A | intron_variant | Intron 1 of 3 | 1 | |||||
P4HA2 | ENST00000431054.5 | c.78+571T>A | intron_variant | Intron 1 of 5 | 4 | ENSP00000391257.1 |
Frequencies
GnomAD3 genomes AF: 0.00208 AC: 317AN: 152198Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000565 AC: 142AN: 251202Hom.: 1 AF XY: 0.000375 AC XY: 51AN XY: 135872
GnomAD4 exome AF: 0.000232 AC: 339AN: 1461846Hom.: 1 Cov.: 31 AF XY: 0.000190 AC XY: 138AN XY: 727232
GnomAD4 genome AF: 0.00209 AC: 318AN: 152316Hom.: 0 Cov.: 32 AF XY: 0.00204 AC XY: 152AN XY: 74474
ClinVar
Submissions by phenotype
SLC22A4-related disorder Benign:1
This variant is classified as likely 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