chr11-36462565-G-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_001160167.2(PRR5L):c.936G>T(p.Leu312=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00239 in 1,612,760 control chromosomes in the GnomAD database, including 82 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.013 ( 47 hom., cov: 32)
Exomes 𝑓: 0.0012 ( 35 hom. )
Consequence
PRR5L
NM_001160167.2 synonymous
NM_001160167.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0410
Genes affected
PRR5L (HGNC:25878): (proline rich 5 like) Enables ubiquitin protein ligase binding activity. Involved in several processes, including TORC2 signaling; positive regulation of mRNA catabolic process; and regulation of fibroblast migration. Part of TORC2 complex. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.58).
BP6
?
Variant 11-36462565-G-T is Benign according to our data. Variant chr11-36462565-G-T is described in ClinVar as [Benign]. Clinvar id is 790088.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.041 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0134 (2042/152288) while in subpopulation AFR AF= 0.0463 (1926/41564). AF 95% confidence interval is 0.0446. There are 47 homozygotes in gnomad4. There are 954 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 47 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRR5L | NM_001160167.2 | c.936G>T | p.Leu312= | synonymous_variant | 9/9 | ENST00000530639.6 | |
PRR5L | NM_024841.5 | c.936G>T | p.Leu312= | synonymous_variant | 10/10 | ||
PRR5L | NM_001160168.2 | c.552G>T | p.Leu184= | synonymous_variant | 6/6 | ||
PRR5L | NM_001160169.1 | c.*191G>T | 3_prime_UTR_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRR5L | ENST00000530639.6 | c.936G>T | p.Leu312= | synonymous_variant | 9/9 | 2 | NM_001160167.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0133 AC: 2031AN: 152170Hom.: 47 Cov.: 32
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GnomAD3 exomes AF: 0.00340 AC: 840AN: 247064Hom.: 14 AF XY: 0.00228 AC XY: 306AN XY: 133982
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GnomAD4 exome AF: 0.00125 AC: 1819AN: 1460472Hom.: 35 Cov.: 30 AF XY: 0.00107 AC XY: 774AN XY: 726508
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GnomAD4 genome ? AF: 0.0134 AC: 2042AN: 152288Hom.: 47 Cov.: 32 AF XY: 0.0128 AC XY: 954AN XY: 74456
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 20, 2018 | - - |
Computational scores
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Name
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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