chr4-88007731-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_000297.4(PKD2):c.-3G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000166 in 1,202,336 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
Genomes: 𝑓 0.0000067 ( 0 hom., cov: 33)
Exomes 𝑓: 9.5e-7 ( 0 hom. )
Consequence
PKD2
NM_000297.4 5_prime_UTR
NM_000297.4 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.256
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 Likely_benign. Variant got -4 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.64).
BP6
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Variant 4-88007731-G-A is Benign according to our data. Variant chr4-88007731-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3029240.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PKD2 | NM_000297.4 | c.-3G>A | 5_prime_UTR_variant | 1/15 | ENST00000237596.7 | ||
PKD2 | XM_011532028.3 | c.-3G>A | 5_prime_UTR_variant | 1/14 | |||
PKD2 | NR_156488.2 | n.97G>A | non_coding_transcript_exon_variant | 1/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PKD2 | ENST00000237596.7 | c.-3G>A | 5_prime_UTR_variant | 1/15 | 1 | NM_000297.4 | P1 | ||
ENST00000662475.1 | n.112+635C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00000668 AC: 1AN: 149672Hom.: 0 Cov.: 33
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GnomAD4 exome AF: 9.50e-7 AC: 1AN: 1052664Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0AN XY: 511974
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
PKD2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 14, 2021 | 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
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at