rs4952590
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_138370.3(PKDCC):c.639+943C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 152,064 control chromosomes in the GnomAD database, including 4,979 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 0.22 ( 4979 hom., cov: 31)
Consequence
PKDCC
NM_138370.3 intron
NM_138370.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.311
Genes affected
PKDCC (HGNC:25123): (protein kinase domain containing, cytoplasmic) Enables non-membrane spanning protein tyrosine kinase activity. Involved in peptidyl-tyrosine phosphorylation and skeletal system development. Located in extracellular region. [provided by Alliance of Genome Resources, Apr 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 (BayesDel_noAF=-0.8).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PKDCC | NM_138370.3 | c.639+943C>T | intron_variant | ENST00000294964.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PKDCC | ENST00000294964.6 | c.639+943C>T | intron_variant | 1 | NM_138370.3 | P1 | |||
PKDCC | ENST00000401498.6 | c.497+943C>T | intron_variant, NMD_transcript_variant | 5 | |||||
PKDCC | ENST00000485578.1 | n.260+943C>T | intron_variant, non_coding_transcript_variant | 2 | |||||
PKDCC | ENST00000492861.1 | n.65+943C>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.221 AC: 33582AN: 151946Hom.: 4951 Cov.: 31
GnomAD3 genomes
?
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33582
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151946
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.221 AC: 33674AN: 152064Hom.: 4979 Cov.: 31 AF XY: 0.221 AC XY: 16464AN XY: 74330
GnomAD4 genome
?
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33674
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152064
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31
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16464
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74330
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1075
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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