rs80338869
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BS1BS2
The NM_025137.4(SPG11):c.7023C>T(p.Tyr2341Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0258 in 1,613,970 control chromosomes in the GnomAD database, including 655 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_025137.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
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SPG11 | NM_025137.4 | c.7023C>T | p.Tyr2341Tyr | synonymous_variant | Exon 39 of 40 | ENST00000261866.12 | NP_079413.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0189 AC: 2879AN: 152132Hom.: 31 Cov.: 32
GnomAD3 exomes AF: 0.0205 AC: 5158AN: 251064Hom.: 73 AF XY: 0.0209 AC XY: 2837AN XY: 135784
GnomAD4 exome AF: 0.0265 AC: 38725AN: 1461720Hom.: 624 Cov.: 32 AF XY: 0.0265 AC XY: 19252AN XY: 727174
GnomAD4 genome AF: 0.0189 AC: 2878AN: 152250Hom.: 31 Cov.: 32 AF XY: 0.0176 AC XY: 1309AN XY: 74452
ClinVar
Submissions by phenotype
Hereditary spastic paraplegia 11 Uncertain:1Benign:3
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This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
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not specified Benign:2
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
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Hereditary spastic paraplegia Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at