rs367983387
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001009944.3(PKD1):c.1710C>T(p.His570=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00638 in 1,540,920 control chromosomes in the GnomAD database, including 44 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0057 ( 2 hom., cov: 33)
Exomes 𝑓: 0.0065 ( 42 hom. )
Consequence
PKD1
NM_001009944.3 synonymous
NM_001009944.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.710
Genes affected
PKD1 (HGNC:9008): (polycystin 1, transient receptor potential channel interacting) This gene encodes a member of the polycystin protein family. The encoded glycoprotein contains a large N-terminal extracellular region, multiple transmembrane domains and a cytoplasmic C-tail. It is an integral membrane protein that functions as a regulator of calcium permeable cation channels and intracellular calcium homoeostasis. It is also involved in cell-cell/matrix interactions and may modulate G-protein-coupled signal-transduction pathways. It plays a role in renal tubular development, and mutations in this gene cause autosomal dominant polycystic kidney disease type 1 (ADPKD1). ADPKD1 is characterized by the growth of fluid-filled cysts that replace normal renal tissue and result in end-stage renal failure. Splice variants encoding different isoforms have been noted for this gene. Also, six pseudogenes, closely linked in a known duplicated region on chromosome 16p, have been described. [provided by RefSeq, Oct 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
?
Variant 16-2116541-G-A is Benign according to our data. Variant chr16-2116541-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 256926.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-2116541-G-A is described in Lovd as [Likely_benign].
BP7
?
Synonymous conserved (PhyloP=-0.71 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00566 (862/152282) while in subpopulation NFE AF= 0.00776 (528/68006). AF 95% confidence interval is 0.00722. There are 2 homozygotes in gnomad4. There are 447 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 862 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PKD1 | NM_001009944.3 | c.1710C>T | p.His570= | synonymous_variant | 8/46 | ENST00000262304.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PKD1 | ENST00000262304.9 | c.1710C>T | p.His570= | synonymous_variant | 8/46 | 1 | NM_001009944.3 | P5 | |
PKD1 | ENST00000423118.5 | c.1710C>T | p.His570= | synonymous_variant | 8/46 | 1 | A2 | ||
PKD1 | ENST00000488185.2 | c.472+948C>T | intron_variant | 5 | |||||
PKD1 | ENST00000568591.5 | c.*38C>T | 3_prime_UTR_variant, NMD_transcript_variant | 4/12 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00566 AC: 862AN: 152164Hom.: 2 Cov.: 33
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GnomAD3 exomes AF: 0.00498 AC: 857AN: 172122Hom.: 6 AF XY: 0.00530 AC XY: 497AN XY: 93836
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GnomAD4 exome AF: 0.00646 AC: 8976AN: 1388638Hom.: 42 Cov.: 30 AF XY: 0.00644 AC XY: 4436AN XY: 688646
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:8
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Polycystic kidney disease, adult type Benign:3
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Sep 23, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | May 23, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Apr 01, 2020 | - - |
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 18, 2020 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | May 01, 2024 | PKD1: BP4, BP7, BS2 - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Feb 01, 2017 | - - |
Polycystic kidney disease Benign:1
Benign, no assertion criteria provided | clinical testing | Department of Pathology and Laboratory Medicine, Sinai Health System | - | The PKD1 p.His570His variant was identified in 8 of 860 proband chromosomes (frequency: 0.009) from individuals or families with ADPKD (Rossetti 2001, Rossetti 2002, Rossetti 2012, Garcia-Gonzalez 2007). The variant was also identified in dbSNP (ID: rs367983387) as “NA”, Clinvitae (classified as variant of unknown significance by Emory Genetics), and in the ADPKD Mutation Database (classification likely neutral); in the 1000 Genomes Project in 17 of 5000 chromosomes (frequency: 0.0034), in HAP-MAP: HAPMAP-EUR in 15 of 1006 chromosomes (frequency: 0.0149), HAPMAP-AMR in 1 of 694 chromosomes (frequency: 0.0014), HAPMAP-EAS in 1 of 1008 chromosomes (frequency: 0.001), NHLBI GO Exome Sequencing Project (ESP) in 40 of 8462 (frequency: 0.0047) European American, and in 3 of 4308 (frequency: 0.0007) African American alleles. The variant was also identified in the Exome Aggregation Consortium database (March 14, 2016) in 19 of 130 chromosomes (frequency: 0.1462) from a population of European (Finnish) individuals, in 164 (2 homozygous) of 7450 chromosomes (frequency: 0.02201) from a population of European (Non-Finnish) individuals, in 34 of 8056 chromosomes (frequency: 0.0042) from a population of South Asians, and in 3 of 1762 chromosomes (frequency: 0.0017) from a population of African individuals, increasing the likelihood this could be a low frequency benign variant. The variant was not seen in the East Asian, Other or Latino poulations. The variant was identified by our laboratory in a patient with PKD with a co-occurring pathogenic PKD1 variant (c.8388T>G, p.Tyr2796X), increasing the likelihood that the p.His570His variant does not have clinical significance. The p.His570His 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. In addition, in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. In summary, based on the above information, this variant meets our laboratory criteria to be classified as benign. - |
PKD1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 20, 2019 | 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:
Name
Calibrated prediction
Score
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at