chr3-149129774-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6BP7
The NM_032383.5(HPS3):c.51C>T(p.Pro17Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00116 in 1,608,694 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_032383.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000900 AC: 137AN: 152194Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000838 AC: 199AN: 237482Hom.: 0 AF XY: 0.000785 AC XY: 102AN XY: 129932
GnomAD4 exome AF: 0.00119 AC: 1730AN: 1456382Hom.: 1 Cov.: 31 AF XY: 0.00117 AC XY: 847AN XY: 724552
GnomAD4 genome AF: 0.000899 AC: 137AN: 152312Hom.: 0 Cov.: 32 AF XY: 0.000886 AC XY: 66AN XY: 74484
ClinVar
Submissions by phenotype
not specified Benign:3
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p.Pro17Pro in exon 1 of HPS3: This variant is not expected to have clinical sign ificance because it does not alter an amino acid residue and is not located with in the splice consensus sequence. It has been identified in 0.1% (111/59912) of European chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broa dinstitute.org; dbSNP rs141883346). -
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Hermansky-Pudlak syndrome 3 Uncertain: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, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. -
Hermansky-Pudlak syndrome Benign:1
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not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at