rs145316065
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_025137.4(SPG11):c.1906C>T(p.Leu636=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000874 in 1,613,192 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. L636L) has been classified as Likely benign.
Frequency
Consequence
NM_025137.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPG11 | NM_025137.4 | c.1906C>T | p.Leu636= | synonymous_variant | 10/40 | ENST00000261866.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPG11 | ENST00000261866.12 | c.1906C>T | p.Leu636= | synonymous_variant | 10/40 | 1 | NM_025137.4 |
Frequencies
GnomAD3 genomes ? AF: 0.000532 AC: 81AN: 152138Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000132 AC: 33AN: 250512Hom.: 2 AF XY: 0.0000591 AC XY: 8AN XY: 135454
GnomAD4 exome AF: 0.0000411 AC: 60AN: 1460936Hom.: 2 Cov.: 32 AF XY: 0.0000303 AC XY: 22AN XY: 726818
GnomAD4 genome ? AF: 0.000532 AC: 81AN: 152256Hom.: 1 Cov.: 32 AF XY: 0.000470 AC XY: 35AN XY: 74462
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 11, 2019 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Hereditary spastic paraplegia 11 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at