NM_003119.4:c.881G>A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_003119.4(SPG7):c.881G>A(p.Arg294His) variant causes a missense change. The variant allele was found at a frequency of 0.002 in 1,614,072 control chromosomes in the GnomAD database, including 61 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_003119.4 missense
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: 0.0107 AC: 1628AN: 152076Hom.: 34 Cov.: 33
GnomAD3 exomes AF: 0.00272 AC: 683AN: 251406Hom.: 10 AF XY: 0.00201 AC XY: 273AN XY: 135886
GnomAD4 exome AF: 0.00109 AC: 1596AN: 1461878Hom.: 27 Cov.: 47 AF XY: 0.000967 AC XY: 703AN XY: 727242
GnomAD4 genome AF: 0.0107 AC: 1631AN: 152194Hom.: 34 Cov.: 33 AF XY: 0.0106 AC XY: 791AN XY: 74434
ClinVar
Submissions by phenotype
Hereditary spastic paraplegia 7 Benign: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). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign. -
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not provided Benign:2
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not specified Benign:1
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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at