15-22786673-C-G
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2
The NM_144599.5(NIPA1):āc.17C>Gā(p.Ala6Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000865 in 1,075,416 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 8/11 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_144599.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000514 AC: 7AN: 136294Hom.: 0 Cov.: 30
GnomAD4 exome AF: 0.0000916 AC: 86AN: 939122Hom.: 0 Cov.: 21 AF XY: 0.0000979 AC XY: 44AN XY: 449314
GnomAD4 genome AF: 0.0000514 AC: 7AN: 136294Hom.: 0 Cov.: 30 AF XY: 0.0000454 AC XY: 3AN XY: 66042
ClinVar
Submissions by phenotype
not specified Uncertain:1
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Hereditary spastic paraplegia 6 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at