4-88007652-G-C
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_000297.4(PKD2):c.-82G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0212 in 941,466 control chromosomes in the GnomAD database, including 267 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.017 ( 33 hom., cov: 33)
Exomes 𝑓: 0.022 ( 234 hom. )
Consequence
PKD2
NM_000297.4 5_prime_UTR
NM_000297.4 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.389
Genes affected
PKD2 (HGNC:9009): (polycystin 2, transient receptor potential cation channel) This gene encodes a member of the polycystin protein family. The encoded protein is a multi-pass membrane protein that functions as a calcium permeable cation channel, and is involved in calcium transport and calcium signaling in renal epithelial cells. This protein interacts with polycystin 1, and they may be partners in a common signaling cascade involved in tubular morphogenesis. Mutations in this gene are associated with autosomal dominant polycystic kidney disease type 2. [provided by RefSeq, Mar 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.71).
BP6
Variant 4-88007652-G-C is Benign according to our data. Variant chr4-88007652-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 350007.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr4-88007652-G-C is described in Lovd as [Benign].
BS1
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0168 (2538/150916) while in subpopulation SAS AF= 0.047 (227/4832). AF 95% confidence interval is 0.042. There are 33 homozygotes in gnomad4. There are 1373 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High AC in GnomAd4 at 2538 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PKD2 | NM_000297.4 | c.-82G>C | 5_prime_UTR_variant | 1/15 | ENST00000237596.7 | NP_000288.1 | ||
PKD2 | XM_011532028.3 | c.-82G>C | 5_prime_UTR_variant | 1/14 | XP_011530330.1 | |||
PKD2 | NR_156488.2 | n.18G>C | non_coding_transcript_exon_variant | 1/14 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0168 AC: 2534AN: 150806Hom.: 33 Cov.: 33
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GnomAD4 exome AF: 0.0220 AC: 17375AN: 790550Hom.: 234 Cov.: 11 AF XY: 0.0221 AC XY: 8260AN XY: 374034
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GnomAD4 genome AF: 0.0168 AC: 2538AN: 150916Hom.: 33 Cov.: 33 AF XY: 0.0186 AC XY: 1373AN XY: 73766
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ClinVar
Significance: Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 23, 2019 | - - |
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Polycystic kidney disease 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | 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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. - |
Computational scores
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BayesDel_noAF
Benign
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Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at