rs121918634
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM2PM5PP3_Strong
The NM_003126.4(SPTA1):āc.779T>Gā(p.Leu260Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000342 in 1,461,496 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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. L260P) has been classified as Likely pathogenic.
Frequency
Consequence
NM_003126.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPTA1 | NM_003126.4 | c.779T>G | p.Leu260Arg | missense_variant | 6/52 | ENST00000643759.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPTA1 | ENST00000643759.2 | c.779T>G | p.Leu260Arg | missense_variant | 6/52 | NM_003126.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000803 AC: 2AN: 249130Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135138
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461496Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 727058
GnomAD4 genome ? Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at