Variant 10-88314383-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000331772.9(RNLS):c.876+83C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 1,371,064 control chromosomes in the GnomAD database, including 81,710 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.30 ( 7394 hom., cov: 32)

Exomes 𝑓: 0.34 ( 74316 hom. )

Consequence

RNLS
ENST00000331772.9 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.254

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]

RNLS links:

LOC101929727 (HGNC:):

LOC101929727 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 10-88314383-G-A is Benign according to our data. Variant chr10-88314383-G-A is described in ClinVar as [Benign]. Clinvar id is 1273084.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RNLS	NM_001031709.3 linkuse as main transcript	c.876+83C>T		intron_variant		ENST00000331772.9	NP_001026879.2
LOC101929727	XR_001747537.3 linkuse as main transcript	n.443-55696G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RNLS	ENST00000331772.9 linkuse as main transcript	c.876+83C>T		intron_variant		1	NM_001031709.3	ENSP00000332530	P1	Q5VYX0-1
RNLS	ENST00000371947.7 linkuse as main transcript	c.876+83C>T		intron_variant		2		ENSP00000361015		Q5VYX0-2

Frequencies

GnomAD3 genomes

AF:

0.303

AC:

45958

AN:

151736

Hom.:

7393

Cov.:

show subpopulations

Gnomad AFR

AF:

0.190

Gnomad AMI

AF:

0.208

Gnomad AMR

AF:

0.314

Gnomad ASJ

AF:

0.310

Gnomad EAS

AF:

0.197

Gnomad SAS

AF:

0.412

Gnomad FIN

AF:

0.407

Gnomad MID

AF:

0.285

Gnomad NFE

AF:

0.355

Gnomad OTH

AF:

0.294

GnomAD4 exome

AF:

0.345

AC:

420360

AN:

1219210

Hom.:

74316

AF XY:

0.348

AC XY:

211962

AN XY:

609350

show subpopulations

Gnomad4 AFR exome

AF:

0.182

Gnomad4 AMR exome

AF:

0.255

Gnomad4 ASJ exome

AF:

0.312

Gnomad4 EAS exome

AF:

0.230

Gnomad4 SAS exome

AF:

0.407

Gnomad4 FIN exome

AF:

0.398

Gnomad4 NFE exome

AF:

0.352

Gnomad4 OTH exome

AF:

0.332

GnomAD4 genome

AF:

0.303

AC:

45995

AN:

151854

Hom.:

7394

Cov.:

AF XY:

0.306

AC XY:

22723

AN XY:

74228

show subpopulations

Gnomad4 AFR

AF:

0.190

Gnomad4 AMR

AF:

0.314

Gnomad4 ASJ

AF:

0.310

Gnomad4 EAS

AF:

0.198

Gnomad4 SAS

AF:

0.412

Gnomad4 FIN

AF:

0.407

Gnomad4 NFE

AF:

0.355

Gnomad4 OTH

AF:

0.295

Alfa

AF:

0.330

Hom.:

1047

Bravo

AF:

0.286

Asia WGS

AF:

0.315

AC:

1098

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 29, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.78

DANN

Benign

0.42

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over