rs9395699
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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.11786-30C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 1,575,624 control chromosomes in the GnomAD database, including 24,270 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.15 ( 1908 hom., cov: 33)
Exomes 𝑓: 0.17 ( 22362 hom. )
Consequence
PKHD1
NM_138694.4 intron
NM_138694.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0380
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=-0.82).
BP6
?
Variant 6-51619550-G-A is Benign according to our data. Variant chr6-51619550-G-A is described in ClinVar as [Benign]. Clinvar id is 262386.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PKHD1 | NM_138694.4 | c.11786-30C>T | intron_variant | ENST00000371117.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PKHD1 | ENST00000371117.8 | c.11786-30C>T | intron_variant | 1 | NM_138694.4 | P2 | |||
ENST00000589278.6 | n.811-2810G>A | intron_variant, non_coding_transcript_variant | 5 | ||||||
ENST00000454361.1 | n.81-2805G>A | intron_variant, non_coding_transcript_variant | 3 | ||||||
ENST00000650088.1 | n.222-2805G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.146 AC: 22195AN: 152016Hom.: 1908 Cov.: 33
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GnomAD3 exomes AF: 0.176 AC: 43306AN: 246564Hom.: 4459 AF XY: 0.179 AC XY: 24004AN XY: 133922
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GnomAD4 exome AF: 0.173 AC: 245822AN: 1423490Hom.: 22362 Cov.: 25 AF XY: 0.174 AC XY: 123577AN XY: 710710
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GnomAD4 genome ? AF: 0.146 AC: 22199AN: 152134Hom.: 1908 Cov.: 33 AF XY: 0.149 AC XY: 11073AN XY: 74356
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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
Benign
DANN
Benign
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