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GeneBe

rs4934396

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001031709.3(RNLS):​c.700+4151T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.067 in 152,266 control chromosomes in the GnomAD database, including 495 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 0.067 ( 495 hom., cov: 32)

Consequence

RNLS
NM_001031709.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.134
Variant links:
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 -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RNLSNM_001031709.3 linkuse as main transcriptc.700+4151T>C intron_variant ENST00000331772.9
LOC101929727XR_001747537.3 linkuse as main transcriptn.443-11678A>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RNLSENST00000331772.9 linkuse as main transcriptc.700+4151T>C intron_variant 1 NM_001031709.3 P1Q5VYX0-1
RNLSENST00000371947.7 linkuse as main transcriptc.700+4151T>C intron_variant 2 Q5VYX0-2
RNLSENST00000466945.5 linkuse as main transcriptn.683+4151T>C intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.0670
AC:
10197
AN:
152148
Hom.:
493
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0154
Gnomad AMI
AF:
0.110
Gnomad AMR
AF:
0.127
Gnomad ASJ
AF:
0.0935
Gnomad EAS
AF:
0.00135
Gnomad SAS
AF:
0.120
Gnomad FIN
AF:
0.0559
Gnomad MID
AF:
0.108
Gnomad NFE
AF:
0.0856
Gnomad OTH
AF:
0.0738
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0670
AC:
10201
AN:
152266
Hom.:
495
Cov.:
32
AF XY:
0.0663
AC XY:
4937
AN XY:
74442
show subpopulations
Gnomad4 AFR
AF:
0.0154
Gnomad4 AMR
AF:
0.127
Gnomad4 ASJ
AF:
0.0935
Gnomad4 EAS
AF:
0.00135
Gnomad4 SAS
AF:
0.121
Gnomad4 FIN
AF:
0.0559
Gnomad4 NFE
AF:
0.0856
Gnomad4 OTH
AF:
0.0730
Alfa
AF:
0.0804
Hom.:
103
Bravo
AF:
0.0705
Asia WGS
AF:
0.0480
AC:
166
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
8.4
DANN
Benign
0.68

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs4934396; hg19: chr10-90118158; API