rs561467860
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_StrongBP6_Very_StrongBP7BS1BS2_Supporting
The NM_001009944.3(PKD1):c.1557C>T(p.Thr519Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000115 in 1,531,962 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001009944.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PKD1 | NM_001009944.3 | c.1557C>T | p.Thr519Thr | synonymous_variant | Exon 7 of 46 | ENST00000262304.9 | NP_001009944.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000164 AC: 25AN: 152228Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000106 AC: 14AN: 132110Hom.: 0 AF XY: 0.000125 AC XY: 9AN XY: 71828
GnomAD4 exome AF: 0.000109 AC: 151AN: 1379616Hom.: 0 Cov.: 30 AF XY: 0.000122 AC XY: 83AN XY: 682060
GnomAD4 genome AF: 0.000164 AC: 25AN: 152346Hom.: 0 Cov.: 33 AF XY: 0.0000805 AC XY: 6AN XY: 74502
ClinVar
Submissions by phenotype
not provided Benign:2
PKD1: BP4, BP7 -
This variant is associated with the following publications: (PMID: 22383692) -
Polycystic kidney disease Uncertain:1
The PKD1 p.Thr519= variant was identified in 1 of 460 proband chromosomes (frequency: 0.002) from individuals or families with autosomal dominant polycystic kidney disease (Rossetti 2012). It was also identified in dbSNP (ID: rs561467860) as "With Likely benign allele", ClinVar (classified as likely benign by Athena Diagnostics Inc.) and in the ADPKD Mutation Database (as likely neutral). The variant was not identified in the LOVD 3.0 or PKD1-LOVD databases. It was identified in control databases in 18 of 158020 chromosomes at a frequency of 0.0001 (Genome Aggregation Database Feb 27, 2017). It was observed in the following populations: European in 16 of 62580 chromosomes (freq: 0.0003) and East Asian in 2 of 11602 chromosomes (freq: 0.0002), while it was not observed in the African, Other, Latino, Ashkenazi Jewish, Finnish, or South Asian populations. In addition, we cannot be certain that data from control databases are specific to PKD1 and not from one of the six PKD1 pseudogenes. The p.Thr519= variant is not expected to have clinical significance because it does not result in a change of amino acid and is not located in a known consensus splice site. However, 1 of 4 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) predicts a greater than 10% difference in splicing; this is not very predictive of pathogenicity. This variant was identified with a co-occurring, pathogenic variant in PKD2 (c.1081C>T, p.Arg361*), increasing the likelihood that this variant does not have clinical significance. In summary, based on the above information, the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance. -
not specified Benign:1
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Polycystic kidney disease, adult type Benign:1
- -
PKD1-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