rs3730102
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000537.4(REN):c.698+111C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 1,407,184 control chromosomes in the GnomAD database, including 13,003 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.14 ( 1552 hom., cov: 32)
Exomes 𝑓: 0.13 ( 11451 hom. )
Consequence
REN
NM_000537.4 intron
NM_000537.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.529
Genes affected
REN (HGNC:9958): (renin) This gene encodes renin, an aspartic protease that is secreted by the kidneys. Renin is a part of the renin-angiotensin-aldosterone system involved in regulation of blood pressure, and electrolyte balance. This enzyme catalyzes the first step in the activation pathway of angiotensinogen by cleaving angiotensinogen to form angiotensin I, which is then converted to angiotensin II by angiotensin I converting enzyme. This cascade can result in aldosterone release, narrowing of blood vessels, and increase in blood pressure as angiotension II is a vasoconstrictive peptide. Transcript variants that encode different protein isoforms and that arise from alternative splicing and the use of alternative promoters have been described, but their full-length nature has not been determined. Mutations in this gene have been shown to cause hyperuricemic nephropathy familial juvenile 2, familial hyperproreninemia, and renal tubular dysgenesis. [provided by RefSeq, May 2020]
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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=-0.94).
BP6
?
Variant 1-204157250-G-A is Benign according to our data. Variant chr1-204157250-G-A is described in ClinVar as [Benign]. Clinvar id is 1281962.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
REN | NM_000537.4 | c.698+111C>T | intron_variant | ENST00000272190.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
REN | ENST00000272190.9 | c.698+111C>T | intron_variant | 1 | NM_000537.4 | P1 | |||
REN | ENST00000638118.1 | c.584+111C>T | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.143 AC: 21692AN: 152100Hom.: 1549 Cov.: 32
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GnomAD4 exome AF: 0.132 AC: 165032AN: 1254966Hom.: 11451 AF XY: 0.131 AC XY: 83045AN XY: 634980
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GnomAD4 genome ? AF: 0.143 AC: 21704AN: 152218Hom.: 1552 Cov.: 32 AF XY: 0.142 AC XY: 10582AN XY: 74438
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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 | May 15, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
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