rs58559714
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_006031.6(PCNT):c.5322G>A(p.Glu1774Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0905 in 1,613,660 control chromosomes in the GnomAD database, including 12,213 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_006031.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.178 AC: 27100AN: 152154Hom.: 4496 Cov.: 34
GnomAD3 exomes AF: 0.0952 AC: 23738AN: 249288Hom.: 2198 AF XY: 0.0905 AC XY: 12234AN XY: 135234
GnomAD4 exome AF: 0.0814 AC: 118934AN: 1461388Hom.: 7712 Cov.: 34 AF XY: 0.0805 AC XY: 58514AN XY: 727006
GnomAD4 genome AF: 0.178 AC: 27139AN: 152272Hom.: 4501 Cov.: 34 AF XY: 0.175 AC XY: 13037AN XY: 74460
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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not provided Benign:2
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Microcephalic osteodysplastic primordial dwarfism type II Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at