Variant 10-88314388-A-G 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+78T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 1,427,590 control chromosomes in the GnomAD database, including 82,316 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.29 ( 6874 hom., cov: 32)

Exomes 𝑓: 0.34 ( 75442 hom. )

Consequence

RNLS
ENST00000331772.9 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.0320

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 10-88314388-A-G is Benign according to our data. Variant chr10-88314388-A-G is described in ClinVar as [Benign]. Clinvar id is 1273010.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.369 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+78T>C		intron_variant		ENST00000331772.9	NP_001026879.2
LOC101929727	XR_001747537.3 linkuse as main transcript	n.443-55691A>G		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+78T>C		intron_variant		1	NM_001031709.3	ENSP00000332530	P1	Q5VYX0-1
RNLS	ENST00000371947.7 linkuse as main transcript	c.876+78T>C		intron_variant		2		ENSP00000361015		Q5VYX0-2

Frequencies

GnomAD3 genomes

AF:

0.285

AC:

43300

AN:

151778

Hom.:

6874

Cov.:

show subpopulations

Gnomad AFR

AF:

0.142

Gnomad AMI

AF:

0.200

Gnomad AMR

AF:

0.305

Gnomad ASJ

AF:

0.293

Gnomad EAS

AF:

0.169

Gnomad SAS

AF:

0.383

Gnomad FIN

AF:

0.403

Gnomad MID

AF:

0.263

Gnomad NFE

AF:

0.353

Gnomad OTH

AF:

0.279

GnomAD4 exome

AF:

0.339

AC:

432948

AN:

1275694

Hom.:

75442

AF XY:

0.341

AC XY:

217011

AN XY:

635650

show subpopulations

Gnomad4 AFR exome

AF:

0.132

Gnomad4 AMR exome

AF:

0.248

Gnomad4 ASJ exome

AF:

0.296

Gnomad4 EAS exome

AF:

0.203

Gnomad4 SAS exome

AF:

0.374

Gnomad4 FIN exome

AF:

0.395

Gnomad4 NFE exome

AF:

0.351

Gnomad4 OTH exome

AF:

0.321

GnomAD4 genome

AF:

0.285

AC:

43330

AN:

151896

Hom.:

6874

Cov.:

AF XY:

0.288

AC XY:

21364

AN XY:

74232

show subpopulations

Gnomad4 AFR

AF:

0.143

Gnomad4 AMR

AF:

0.305

Gnomad4 ASJ

AF:

0.293

Gnomad4 EAS

AF:

0.170

Gnomad4 SAS

AF:

0.384

Gnomad4 FIN

AF:

0.403

Gnomad4 NFE

AF:

0.353

Gnomad4 OTH

AF:

0.280

Alfa

AF:

0.318

Hom.:

1004

Bravo

AF:

0.267

Asia WGS

AF:

0.288

AC:

1006

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

1.4

DANN

Benign

0.60

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.

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