rs377135175
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_025137.4(SPG11):c.21C>T(p.Val7=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000244 in 1,595,770 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. V7V) has been classified as Likely benign.
Frequency
Consequence
NM_025137.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPG11 | NM_025137.4 | c.21C>T | p.Val7= | synonymous_variant | 1/40 | ENST00000261866.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPG11 | ENST00000261866.12 | c.21C>T | p.Val7= | synonymous_variant | 1/40 | 1 | NM_025137.4 |
Frequencies
GnomAD3 genomes AF: 0.0000788 AC: 12AN: 152230Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000422 AC: 9AN: 213348Hom.: 0 AF XY: 0.0000421 AC XY: 5AN XY: 118686
GnomAD4 exome AF: 0.0000180 AC: 26AN: 1443422Hom.: 0 Cov.: 32 AF XY: 0.00000836 AC XY: 6AN XY: 717762
GnomAD4 genome AF: 0.0000853 AC: 13AN: 152348Hom.: 0 Cov.: 32 AF XY: 0.000107 AC XY: 8AN XY: 74492
ClinVar
Submissions by phenotype
Hereditary spastic paraplegia 11 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 19, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at