chr10-88274731-A-G

Position:

• chr10-88274731-A-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The XR_001747537.3(LOC101929727):​n.443-95348A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.857 in 407,610 control chromosomes in the GnomAD database, including 150,328 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.84 (53484 hom., cov: 31)
  • Exomes 𝑓: 0.87 (96844 hom.)
• Consequence: LOC101929727 XR_001747537.3 intron, non_coding_transcript
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.371

Genes affected

LOC101929727 (HGNC:):

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]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BP6: Variant 10-88274731-A-G is Benign according to our data. Variant chr10-88274731-A-G is described in ClinVar as [Benign]. Clinvar id is 1232021.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.88 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101929727	XR_001747537.3	n.443-95348A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RNLS	ENST00000371947.7	c.*230T>C		3_prime_UTR_variant	7/7	2

Frequencies

GnomAD3 genomes AF: 0.836 AC: 127052 AN: 151944 Hom.: 53450 Cov.: 31

Gnomad AFR AF: 0.742

Gnomad AMI AF: 0.830

Gnomad AMR AF: 0.839

Gnomad ASJ AF: 0.828

Gnomad EAS AF: 0.796

Gnomad SAS AF: 0.862

Gnomad FIN AF: 0.891

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.886

Gnomad OTH AF: 0.840

GnomAD4 exome AF: 0.870 AC: 222214 AN: 255548 Hom.: 96844 Cov.: 2 AF XY: 0.870 AC XY: 117968 AN XY: 135620

Gnomad4 AFR exome AF: 0.741

Gnomad4 AMR exome AF: 0.845

Gnomad4 ASJ exome AF: 0.837

Gnomad4 EAS exome AF: 0.816

Gnomad4 SAS exome AF: 0.860

Gnomad4 FIN exome AF: 0.895

Gnomad4 NFE exome AF: 0.887

Gnomad4 OTH exome AF: 0.864

GnomAD4 genome AF: 0.836 AC: 127148 AN: 152062 Hom.: 53484 Cov.: 31 AF XY: 0.835 AC XY: 62074 AN XY: 74300

Gnomad4 AFR AF: 0.742

Gnomad4 AMR AF: 0.839

Gnomad4 ASJ AF: 0.828

Gnomad4 EAS AF: 0.797

Gnomad4 SAS AF: 0.862

Gnomad4 FIN AF: 0.891

Gnomad4 NFE AF: 0.886

Gnomad4 OTH AF: 0.841

Alfa AF: 0.875 Hom.: 81811

Bravo AF: 0.828

Asia WGS AF: 0.826 AC: 2870 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

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	-0.98
CADD	Benign	1.8
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10749568; hg19: chr10-90034488;