NM_001611.5:c.814C>T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_001611.5(ACP5):c.814C>T(p.Arg272Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00413 in 1,614,120 control chromosomes in the GnomAD database, including 23 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 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_001611.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ACP5 | NM_001611.5 | c.814C>T | p.Arg272Cys | missense_variant | Exon 5 of 5 | ENST00000648477.1 | NP_001602.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00334 AC: 508AN: 152180Hom.: 2 Cov.: 31
GnomAD3 exomes AF: 0.00315 AC: 792AN: 251074Hom.: 3 AF XY: 0.00321 AC XY: 436AN XY: 135808
GnomAD4 exome AF: 0.00421 AC: 6157AN: 1461822Hom.: 21 Cov.: 31 AF XY: 0.00410 AC XY: 2983AN XY: 727204
GnomAD4 genome AF: 0.00334 AC: 508AN: 152298Hom.: 2 Cov.: 31 AF XY: 0.00309 AC XY: 230AN XY: 74452
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:5
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Has not been previously published as pathogenic or benign to our knowledge; In silico analysis supports that this missense variant has a deleterious effect on protein structure/function -
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ACP5: BP4, BS2 -
Spondyloenchondrodysplasia with immune dysregulation Uncertain:1Benign:1
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ACP5 NM_001111035.2 exon 7 p.Arg272Cys (c.814C>T): This variant has not been reported in the literature but is present in 0.4% (595/126376) of European alleles, including 3 homozygotes, in the Genome Aggregation Database (http://gnomad.broadinstitute.org/variant/19-11685989-G-A). This variant is present in ClinVar, with several labs classifying this variant as likely benign or benign (Variation ID:198455). Evolutionary conservation and computational predictive tools for this variant are unclear. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain. -
not specified Benign:2
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BS1, BS2, BP6; This alteration has an allele frequency that is greater than expected for the associated disease, was seen in a healthy adult where full penetrance of the disorder is expected at an early age, and was reported as a benign/likely benign alteration by a reputable source (ClinVar or other correspondence from a clinical testing laboratory). -
ACP5-related disorder Benign:1
This variant is classified as likely 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