rs200817545
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM1PM2PM5
The NM_001126108.2(SLC12A3):c.1276A>C(p.Asn426His) variant causes a missense change. The variant allele was found at a frequency of 0.00000186 in 1,612,092 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. N426Y) has been classified as Pathogenic.
Frequency
Consequence
NM_001126108.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC12A3 | NM_001126108.2 | c.1276A>C | p.Asn426His | missense_variant | 10/26 | ENST00000563236.6 | |
SLC12A3 | NM_000339.3 | c.1276A>C | p.Asn426His | missense_variant | 10/26 | ||
SLC12A3 | NM_001126107.2 | c.1273A>C | p.Asn425His | missense_variant | 10/26 | ||
SLC12A3 | NM_001410896.1 | c.1273A>C | p.Asn425His | missense_variant | 10/26 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC12A3 | ENST00000563236.6 | c.1276A>C | p.Asn426His | missense_variant | 10/26 | 1 | NM_001126108.2 | A1 | |
SLC12A3 | ENST00000438926.6 | c.1276A>C | p.Asn426His | missense_variant | 10/26 | 1 | A1 | ||
SLC12A3 | ENST00000566786.5 | c.1273A>C | p.Asn425His | missense_variant | 10/26 | 1 | P4 | ||
SLC12A3 | ENST00000262502.5 | c.1273A>C | p.Asn425His | missense_variant | 10/26 | 5 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152092Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000404 AC: 1AN: 247430Hom.: 0 AF XY: 0.00000743 AC XY: 1AN XY: 134634
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460000Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 726378
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152092Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74308
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at