NM_025233.7:c.1486-5C>G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_025233.7(COASY):c.1486-5C>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0554 in 1,614,024 control chromosomes in the GnomAD database, including 2,875 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_025233.7 splice_region, 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: 0.0433 AC: 6593AN: 152212Hom.: 192 Cov.: 33
GnomAD3 exomes AF: 0.0478 AC: 12018AN: 251174Hom.: 382 AF XY: 0.0498 AC XY: 6759AN XY: 135766
GnomAD4 exome AF: 0.0567 AC: 82902AN: 1461694Hom.: 2684 Cov.: 33 AF XY: 0.0567 AC XY: 41241AN XY: 727140
GnomAD4 genome AF: 0.0432 AC: 6587AN: 152330Hom.: 191 Cov.: 33 AF XY: 0.0421 AC XY: 3134AN XY: 74492
ClinVar
Submissions by phenotype
not specified Benign:2
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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. -
not provided Benign:2
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Neurodegeneration with brain iron accumulation 6 Benign:1
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COASY-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at