10-100288512-G-A
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_016112.3(PKD2L1):c.2336-34C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0478 in 1,306,946 control chromosomes in the GnomAD database, including 1,692 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 0.063 ( 340 hom., cov: 32)
Exomes 𝑓: 0.046 ( 1352 hom. )
Consequence
PKD2L1
NM_016112.3 intron
NM_016112.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.821
Genes affected
PKD2L1 (HGNC:9011): (polycystin 2 like 1, transient receptor potential cation channel) This gene encodes a member of the polycystin protein family. The encoded protein contains multiple transmembrane domains, and cytoplasmic N- and C-termini. The protein may be an integral membrane protein involved in cell-cell/matrix interactions. This protein functions as a calcium-regulated nonselective cation channel. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]
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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=-0.85).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0926 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PKD2L1 | NM_016112.3 | c.2336-34C>T | intron_variant | ENST00000318222.4 | |||
PKD2L1 | NM_001253837.2 | c.2195-34C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PKD2L1 | ENST00000318222.4 | c.2336-34C>T | intron_variant | 1 | NM_016112.3 | P1 | |||
PKD2L1 | ENST00000528248.1 | c.*2076-34C>T | intron_variant, NMD_transcript_variant | 1 | |||||
PKD2L1 | ENST00000465680.2 | c.105-34C>T | intron_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0627 AC: 9532AN: 152058Hom.: 340 Cov.: 32
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GnomAD3 exomes AF: 0.0517 AC: 12820AN: 248012Hom.: 371 AF XY: 0.0511 AC XY: 6872AN XY: 134472
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GnomAD4 exome AF: 0.0459 AC: 52975AN: 1154770Hom.: 1352 Cov.: 16 AF XY: 0.0463 AC XY: 27289AN XY: 589194
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GnomAD4 genome AF: 0.0627 AC: 9539AN: 152176Hom.: 340 Cov.: 32 AF XY: 0.0630 AC XY: 4689AN XY: 74400
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
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