rs144804884
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_025137.4(SPG11):c.2560G>A(p.Ala854Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000353 in 1,613,844 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A854V) has been classified as Uncertain significance.
Frequency
Consequence
NM_025137.4 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 |
---|---|---|---|---|---|---|---|
SPG11 | NM_025137.4 | c.2560G>A | p.Ala854Thr | missense_variant | 14/40 | ENST00000261866.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPG11 | ENST00000261866.12 | c.2560G>A | p.Ala854Thr | missense_variant | 14/40 | 1 | NM_025137.4 |
Frequencies
GnomAD3 genomes AF: 0.000223 AC: 34AN: 152132Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000517 AC: 13AN: 251270Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135794
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1461712Hom.: 0 Cov.: 31 AF XY: 0.0000151 AC XY: 11AN XY: 727176
GnomAD4 genome AF: 0.000223 AC: 34AN: 152132Hom.: 0 Cov.: 32 AF XY: 0.000256 AC XY: 19AN XY: 74326
ClinVar
Submissions by phenotype
Hereditary spastic paraplegia 11 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 28, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at