chr11-62984452-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_153276.3(SLC22A6):c.239G>A(p.Arg80His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000403 in 1,613,780 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_153276.3 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 |
---|---|---|---|---|---|---|---|
SLC22A6 | NM_153276.3 | c.239G>A | p.Arg80His | missense_variant | 1/10 | ENST00000360421.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC22A6 | ENST00000360421.9 | c.239G>A | p.Arg80His | missense_variant | 1/10 | 1 | NM_153276.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152084Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000104 AC: 26AN: 250512Hom.: 0 AF XY: 0.000133 AC XY: 18AN XY: 135480
GnomAD4 exome AF: 0.0000410 AC: 60AN: 1461696Hom.: 0 Cov.: 33 AF XY: 0.0000440 AC XY: 32AN XY: 727138
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152084Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74282
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 17, 2023 | The c.239G>A (p.R80H) alteration is located in exon 1 (coding exon 1) of the SLC22A6 gene. This alteration results from a G to A substitution at nucleotide position 239, causing the arginine (R) at amino acid position 80 to be replaced by a histidine (H). 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