chr6-52048455-T-A
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_138694.4(PKHD1):c.2407+37A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000691 in 1,606,112 control chromosomes in the GnomAD database, including 15 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0038 ( 10 hom., cov: 32)
Exomes 𝑓: 0.00037 ( 5 hom. )
Consequence
PKHD1
NM_138694.4 intron
NM_138694.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.28
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 -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
Variant 6-52048455-T-A is Benign according to our data. Variant chr6-52048455-T-A is described in ClinVar as [Likely_benign]. Clinvar id is 262395.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAd4 at 10 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PKHD1 | NM_138694.4 | c.2407+37A>T | intron_variant | ENST00000371117.8 | NP_619639.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PKHD1 | ENST00000371117.8 | c.2407+37A>T | intron_variant | 1 | NM_138694.4 | ENSP00000360158.3 | ||||
PKHD1 | ENST00000340994.4 | c.2407+37A>T | intron_variant | 5 | ENSP00000341097.4 |
Frequencies
GnomAD3 genomes AF: 0.00380 AC: 579AN: 152180Hom.: 10 Cov.: 32
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GnomAD3 exomes AF: 0.00103 AC: 259AN: 251430Hom.: 1 AF XY: 0.000765 AC XY: 104AN XY: 135886
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GnomAD4 exome AF: 0.000366 AC: 532AN: 1453814Hom.: 5 Cov.: 31 AF XY: 0.000326 AC XY: 236AN XY: 723948
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GnomAD4 genome AF: 0.00380 AC: 578AN: 152298Hom.: 10 Cov.: 32 AF XY: 0.00381 AC XY: 284AN XY: 74466
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
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Benign
CADD
Benign
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