rs628031
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003057.3(SLC22A1):āc.1222A>Cā(p.Met408Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00003 in 1,565,998 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M408V) has been classified as Benign.
Frequency
Consequence
NM_003057.3 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 | UniProt |
---|---|---|---|---|---|---|---|
SLC22A1 | NM_003057.3 | c.1222A>C | p.Met408Leu | missense_variant | 7/11 | ENST00000366963.9 | |
SLC22A1 | NM_153187.2 | c.1222A>C | p.Met408Leu | missense_variant | 7/10 | ||
SLC22A1 | XM_005267103.3 | c.1222A>C | p.Met408Leu | missense_variant | 7/12 | ||
SLC22A1 | XM_006715552.3 | c.1222A>C | p.Met408Leu | missense_variant | 7/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC22A1 | ENST00000366963.9 | c.1222A>C | p.Met408Leu | missense_variant | 7/11 | 1 | NM_003057.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000185 AC: 28AN: 151700Hom.: 0 Cov.: 29
GnomAD3 exomes AF: 0.0000534 AC: 11AN: 205896Hom.: 0 AF XY: 0.0000355 AC XY: 4AN XY: 112662
GnomAD4 exome AF: 0.0000134 AC: 19AN: 1414298Hom.: 0 Cov.: 50 AF XY: 0.0000143 AC XY: 10AN XY: 700082
GnomAD4 genome ? AF: 0.000185 AC: 28AN: 151700Hom.: 0 Cov.: 29 AF XY: 0.000176 AC XY: 13AN XY: 74024
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at