rs202209866
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_014946.4(SPAST):c.683-9C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00132 in 1,612,488 control chromosomes in the GnomAD database, including 28 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_014946.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00110 AC: 168AN: 152064Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00238 AC: 597AN: 250864Hom.: 5 AF XY: 0.00319 AC XY: 433AN XY: 135798
GnomAD4 exome AF: 0.00135 AC: 1968AN: 1460306Hom.: 26 Cov.: 31 AF XY: 0.00181 AC XY: 1318AN XY: 726592
GnomAD4 genome AF: 0.00110 AC: 167AN: 152182Hom.: 2 Cov.: 32 AF XY: 0.00138 AC XY: 103AN XY: 74402
ClinVar
Submissions by phenotype
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 4 Benign:2
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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 allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at