6-52048442-G-A
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_138694.4(PKHD1):c.2407+50C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.49 in 1,569,940 control chromosomes in the GnomAD database, including 196,477 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.41 ( 14955 hom., cov: 32)
Exomes 𝑓: 0.50 ( 181522 hom. )
Consequence
PKHD1
NM_138694.4 intron
NM_138694.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.362
Genes affected
PKHD1 (HGNC:9016): (PKHD1 ciliary IPT domain containing fibrocystin/polyductin) The protein encoded by this gene is predicted to have a single transmembrane (TM)-spanning domain and multiple copies of an immunoglobulin-like plexin-transcription-factor domain. Alternative splicing results in two transcript variants encoding different isoforms. Other alternatively spliced transcripts have been described, but the full length sequences have not been determined. Several of these transcripts are predicted to encode truncated products which lack the TM and may be secreted. Mutations in this gene cause autosomal recessive polycystic kidney disease, also known as polycystic kidney and hepatic disease-1. [provided by RefSeq, Jul 2008]
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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=-0.89).
BP6
Variant 6-52048442-G-A is Benign according to our data. Variant chr6-52048442-G-A is described in ClinVar as [Benign]. Clinvar id is 262396.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.412 AC: 62597AN: 151926Hom.: 14956 Cov.: 32
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GnomAD3 exomes AF: 0.476 AC: 119662AN: 251340Hom.: 30617 AF XY: 0.470 AC XY: 63833AN XY: 135840
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GnomAD4 exome AF: 0.498 AC: 706216AN: 1417894Hom.: 181522 Cov.: 24 AF XY: 0.495 AC XY: 350334AN XY: 708174
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GnomAD4 genome AF: 0.412 AC: 62599AN: 152046Hom.: 14955 Cov.: 32 AF XY: 0.409 AC XY: 30396AN XY: 74316
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Autosomal recessive polycystic kidney disease Benign:1
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | Apr 12, 2018 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 09, 2018 | - - |
Polycystic kidney disease 4 Benign:1
Benign, criteria provided, single submitter | clinical testing | Pars Genome Lab | Jun 19, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at