chr16-71947511-CTTTG-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_181536.2(PKD1L3):c.3695_3698delCAAA(p.Thr1232ArgfsTer26) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 1,541,564 control chromosomes in the GnomAD database, including 51,023 homozygotes. Variant has been reported in ClinVar as Benign (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: 𝑓 0.27 ( 6283 hom., cov: 19)
Exomes 𝑓: 0.25 ( 44740 hom. )
Consequence
PKD1L3
NM_181536.2 frameshift
NM_181536.2 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.794
Genes affected
PKD1L3 (HGNC:21716): (polycystin 1 like 3, transient receptor potential channel interacting) This gene encodes a member of the polycystin protein family. The encoded protein contains 11 transmembrane domains, a latrophilin/CL-1-like GPCR proteolytic site (GPS) domain, and a polycystin-1, lipoxygenase, alpha-toxin (PLAT) domain. This protein may function as a component of cation channel pores.[provided by RefSeq, Apr 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 16-71947511-CTTTG-C is Benign according to our data. Variant chr16-71947511-CTTTG-C is described in ClinVar as [Benign]. Clinvar id is 769495.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.274 AC: 41584AN: 151652Hom.: 6271 Cov.: 19
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GnomAD4 exome AF: 0.246 AC: 342054AN: 1389792Hom.: 44740 AF XY: 0.243 AC XY: 166477AN XY: 686050
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GnomAD4 genome AF: 0.274 AC: 41628AN: 151772Hom.: 6283 Cov.: 19 AF XY: 0.265 AC XY: 19693AN XY: 74182
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ClinVar
Significance: Benign
Submissions summary: Uncertain:1Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Essential tremor Uncertain:1
Uncertain significance, no assertion criteria provided | research | University of Washington Center for Mendelian Genomics, University of Washington | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Nov 15, 2018 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at