6-160258513-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003058.4(SLC22A2):c.245G>A(p.Gly82Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000415 in 1,614,056 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003058.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC22A2 | NM_003058.4 | c.245G>A | p.Gly82Asp | missense_variant | 1/11 | ENST00000366953.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC22A2 | ENST00000366953.8 | c.245G>A | p.Gly82Asp | missense_variant | 1/11 | 1 | NM_003058.4 | P1 | |
SLC22A2 | ENST00000366952.1 | c.182G>A | p.Gly61Asp | missense_variant | 3/8 | 5 | |||
SLC22A2 | ENST00000489644.1 | n.227G>A | non_coding_transcript_exon_variant | 1/2 | 3 | ||||
SLC22A2 | ENST00000491092.1 | n.246G>A | non_coding_transcript_exon_variant | 1/10 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152230Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 251050Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135678
GnomAD4 exome AF: 0.0000438 AC: 64AN: 1461826Hom.: 0 Cov.: 32 AF XY: 0.0000413 AC XY: 30AN XY: 727224
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152230Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 19, 2022 | The c.245G>A (p.G82D) alteration is located in exon 1 (coding exon 1) of the SLC22A2 gene. This alteration results from a G to A substitution at nucleotide position 245, causing the glycine (G) at amino acid position 82 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at