10-88275225-AT-A

Position:

• chr10-88275225-AT-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The XR_001747537.3(LOC101929727):​n.443-94852del 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 0.245 in 152,042 control chromosomes in the GnomAD database, including 4,607 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.24 (4607 hom., cov: 24)
• Consequence: LOC101929727 XR_001747537.3 intron, non_coding_transcript
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0850

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 -10 ACMG points.

• BP6: Variant 10-88275225-AT-A is Benign according to our data. Variant chr10-88275225-AT-A is described in ClinVar as [Benign]. Clinvar id is 1279237.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC101929727	XR_001747537.3	n.443-94852del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RNLS	ENST00000371947.7	c.877-194del		intron_variant		2		ENSP00000361015

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37141 AN: 151924 Hom.: 4599 Cov.: 24

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.245

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.245 AC: 37195 AN: 152042 Hom.: 4607 Cov.: 24 AF XY: 0.242 AC XY: 17961 AN XY: 74314

Gnomad4 AFR AF: 0.252

Gnomad4 AMR AF: 0.207

Gnomad4 ASJ AF: 0.228

Gnomad4 EAS AF: 0.204

Gnomad4 SAS AF: 0.270

Gnomad4 FIN AF: 0.210

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.249

Alfa AF: 0.252 Hom.: 624

Bravo AF: 0.245

Asia WGS AF: 0.281 AC: 978 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

Jul 31, 2018

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs112956101; hg19: chr10-90034982;