rs157069

chr5-54151696-G-Achr5-54151696-G-T

Variant summary

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

The NM_019087.3(ARL15):c.253+2884C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 151,878 control chromosomes in the GnomAD database, including 4,036 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 0.21 (4036 hom., cov: 31)
• Consequence: ARL15 NM_019087.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0440

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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARL15	NM_019087.3	c.253+2884C>T		intron_variant		ENST00000504924.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARL15	ENST00000504924.6	c.253+2884C>T		intron_variant		1	NM_019087.3	P1

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31721 AN: 151762 Hom.: 4025 Cov.: 31

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.0396

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.683

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.209 AC: 31753 AN: 151878 Hom.: 4036 Cov.: 31 AF XY: 0.215 AC XY: 15959 AN XY: 74230

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.160

Gnomad4 EAS AF: 0.683

Gnomad4 SAS AF: 0.359

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.216

Alfa AF: 0.184 Hom.: 264

Bravo AF: 0.214

Asia WGS AF: 0.517 AC: 1792 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.0
Dann	Benign	0.63

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: rs157069; hg19: chr5-53447526;