rs16882423

chr5-54196267-C-A

Variant summary

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

The NM_019087.3(ARL15):c.49-24339G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 151,932 control chromosomes in the GnomAD database, including 5,242 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 0.25 (5242 hom., cov: 32)
• Consequence: ARL15 NM_019087.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00

Genes affected

ARL15 (HGNC:25945): (ADP ribosylation factor like GTPase 15) Predicted to enable GTP binding activity and GTPase activity. Located in extracellular exosome. [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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARL15	NM_019087.3	c.49-24339G>T		intron_variant		ENST00000504924.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARL15	ENST00000504924.6	c.49-24339G>T		intron_variant		1	NM_019087.3	P1

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37987 AN: 151814 Hom.: 5238 Cov.: 32

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.00271

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.250 AC: 38017 AN: 151932 Hom.: 5242 Cov.: 32 AF XY: 0.245 AC XY: 18169 AN XY: 74224

Gnomad4 AFR AF: 0.352

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.279

Gnomad4 EAS AF: 0.00271

Gnomad4 SAS AF: 0.185

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.226

Gnomad4 OTH AF: 0.263

Alfa AF: 0.250 Hom.: 746

Bravo AF: 0.254

Asia WGS AF: 0.110 AC: 385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.49
Dann	Benign	0.56

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

Other links and lift over

dbSNP: rs16882423; hg19: chr5-53492097;