chr6-51830998-TA-T
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The ENST00000371117.8(PKHD1):c.8174-10del variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000767 in 1,603,912 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000084 ( 0 hom. )
Consequence
PKHD1
ENST00000371117.8 splice_polypyrimidine_tract, intron
ENST00000371117.8 splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.74
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 Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 6-51830998-TA-T is Benign according to our data. Variant chr6-51830998-TA-T is described in ClinVar as [Likely_benign]. Clinvar id is 706495.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PKHD1 | NM_138694.4 | c.8174-10del | splice_polypyrimidine_tract_variant, intron_variant | ENST00000371117.8 | NP_619639.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PKHD1 | ENST00000371117.8 | c.8174-10del | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_138694.4 | ENSP00000360158 | P2 | |||
PKHD1 | ENST00000340994.4 | c.8174-10del | splice_polypyrimidine_tract_variant, intron_variant | 5 | ENSP00000341097 | A2 |
Frequencies
GnomAD3 genomes AF: 0.00000659 AC: 1AN: 151716Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.0000840 AC: 122AN: 1452196Hom.: 0 Cov.: 29 AF XY: 0.0000719 AC XY: 52AN XY: 722760
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GnomAD4 genome AF: 0.00000659 AC: 1AN: 151716Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74068
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Autosomal recessive polycystic kidney disease Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Sep 28, 2021 | - - |
PKHD1-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 04, 2022 | 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). - |
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at