rs318699

Positions:

• chr19-11390564-A-G
• chr19-11390564-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.727 in 151,520 control chromosomes in the GnomAD database, including 41,107 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 0.73 (41107 hom., cov: 28)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.789

Genes affected

(HGNC:):

RGL3 (HGNC:30282): (ral guanine nucleotide dissociation stimulator like 3) Predicted to enable guanyl-nucleotide exchange factor activity and small GTPase binding activity. Predicted to be involved in positive regulation of GTPase activity and small GTPase mediated signal transduction. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.908 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.11390564A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RGL3	ENST00000562663.5	n.*1249-5920T>C		intron_variant		5		ENSP00000454678.1
RGL3	ENST00000563726.5	n.*1656-5920T>C		intron_variant		2		ENSP00000455922.1

Frequencies

GnomAD3 genomes AF: 0.727 AC: 110025 AN: 151402 Hom.: 41054 Cov.: 28

Gnomad AFR AF: 0.916

Gnomad AMI AF: 0.484

Gnomad AMR AF: 0.727

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.682

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.650

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.724

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

GnomAD4 genome AF: 0.727 AC: 110143 AN: 151520 Hom.: 41107 Cov.: 28 AF XY: 0.727 AC XY: 53751 AN XY: 73984

Gnomad4 AFR AF: 0.916

Gnomad4 AMR AF: 0.727

Gnomad4 ASJ AF: 0.636

Gnomad4 EAS AF: 0.682

Gnomad4 SAS AF: 0.667

Gnomad4 FIN AF: 0.650

Gnomad4 NFE AF: 0.640

Gnomad4 OTH AF: 0.723

Alfa AF: 0.657 Hom.: 43165

Bravo AF: 0.742

Asia WGS AF: 0.719 AC: 2503 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.92
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs318699; hg19: chr19-11501240;