rs9935113
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000531391.5(PKD1L2):c.298G>T(p.Gly100Cys) variant causes a missense change. The variant allele was found at a frequency of 0.18 in 1,613,554 control chromosomes in the GnomAD database, including 27,320 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.20 ( 3148 hom., cov: 31)
Exomes 𝑓: 0.18 ( 24172 hom. )
Consequence
PKD1L2
ENST00000531391.5 missense
ENST00000531391.5 missense
Scores
2
3
8
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.19
Genes affected
PKD1L2 (HGNC:21715): (polycystin 1 like 2 (gene/pseudogene)) This gene encodes a member of the polycystin protein family. This protein may function as a G-protein-coupled component or regulator of cation channel pores. The long isoform of this protein contains 11 transmembrane domains, a latrophilin/CL-1-like GPCR proteolytic site (GPS) domain, and a polycystin-1, lipoxygenase, alpha-toxin (PLAT) domain. Alternative splicing results in multiple transcript variants encoding distinct isoforms. This gene is a polymorphic pseudogene in humans. [provided by RefSeq, May 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.001959771).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PKD1L2 | NR_126532.3 | n.2368G>T | non_coding_transcript_exon_variant | 14/43 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PKD1L2 | ENST00000525539.5 | c.2353G>T | p.Gly785Cys | missense_variant | 14/43 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.196 AC: 29723AN: 151780Hom.: 3138 Cov.: 31
GnomAD3 genomes
?
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29723
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31
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GnomAD3 exomes AF: 0.184 AC: 45775AN: 248896Hom.: 4570 AF XY: 0.185 AC XY: 24925AN XY: 135094
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GnomAD4 exome AF: 0.178 AC: 259960AN: 1461656Hom.: 24172 Cov.: 32 AF XY: 0.179 AC XY: 130391AN XY: 727140
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GnomAD4 genome ? AF: 0.196 AC: 29754AN: 151898Hom.: 3148 Cov.: 31 AF XY: 0.194 AC XY: 14364AN XY: 74232
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628
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690
ESP6500AA
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1011
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1412
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22322
Asia WGS
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635
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3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Uncertain
DANN
Uncertain
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationTaster
Benign
P;P;P
PrimateAI
Benign
T
PROVEAN
Pathogenic
D;D
REVEL
Pathogenic
Polyphen
1.0
.;D
Vest4
ClinPred
T
GERP RS
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