7-47792717-G-T
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_138295.5(PKD1L1):c.8436C>A(p.Leu2812=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000582 in 1,613,990 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000057 ( 0 hom. )
Consequence
PKD1L1
NM_138295.5 synonymous
NM_138295.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.930
Genes affected
PKD1L1 (HGNC:18053): (polycystin 1 like 1, transient receptor potential channel interacting) This gene encodes a member of the polycystin protein family containing 11 transmembrane domains, a receptor for egg jelly (REJ) domain, and a polycystin-1, lipoxygenase, alpha-toxin (PLAT) domain. The encoded protein may play a role in the male reproductive system. Alternative splice variants have been described but their biological nature has not been determined. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
Variant 7-47792717-G-T is Benign according to our data. Variant chr7-47792717-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 757820.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.93 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PKD1L1 | NM_138295.5 | c.8436C>A | p.Leu2812= | synonymous_variant | 56/57 | ENST00000289672.7 | |
PKD1L1 | XM_017011798.3 | c.8613C>A | p.Leu2871= | synonymous_variant | 57/59 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PKD1L1 | ENST00000289672.7 | c.8436C>A | p.Leu2812= | synonymous_variant | 56/57 | 1 | NM_138295.5 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152188Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000557 AC: 14AN: 251360Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135846
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GnomAD4 exome AF: 0.0000575 AC: 84AN: 1461802Hom.: 0 Cov.: 30 AF XY: 0.0000468 AC XY: 34AN XY: 727204
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GnomAD4 genome AF: 0.0000657 AC: 10AN: 152188Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74350
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 26, 2018 | - - |
Computational scores
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Benign
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Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at