10-88285755-G-A
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The ENST00000331772.9(RNLS):c.877-249C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0706 in 152,094 control chromosomes in the GnomAD database, including 579 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.071 ( 579 hom., cov: 32)
Consequence
RNLS
ENST00000331772.9 intron
ENST00000331772.9 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.143
Genes affected
RNLS (HGNC:25641): (renalase, FAD dependent amine oxidase) Enables several functions, including NADH binding activity; epinephrine binding activity; and monoamine oxidase activity. Involved in negative regulation of blood pressure and negative regulation of heart rate. Located in extracellular region. Implicated in essential hypertension and hypertension. Biomarker of end stage renal disease. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BP6
Variant 10-88285755-G-A is Benign according to our data. Variant chr10-88285755-G-A is described in ClinVar as [Benign]. Clinvar id is 1274833.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.148 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RNLS | NM_001031709.3 | c.877-249C>T | intron_variant | ENST00000331772.9 | NP_001026879.2 | |||
LOC101929727 | XR_001747537.3 | n.443-84324G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RNLS | ENST00000331772.9 | c.877-249C>T | intron_variant | 1 | NM_001031709.3 | ENSP00000332530 | P1 | |||
RNLS | ENST00000371947.7 | c.877-10723C>T | intron_variant | 2 | ENSP00000361015 |
Frequencies
GnomAD3 genomes AF: 0.0705 AC: 10711AN: 151976Hom.: 580 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0706 AC: 10731AN: 152094Hom.: 579 Cov.: 32 AF XY: 0.0694 AC XY: 5159AN XY: 74352
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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 | GeneDx | Jun 28, 2018 | - - |
Computational scores
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Name
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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