5-54084725-T-C

Position:

• chr5-54084725-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_019087.3(ARL15):​c.462+28477A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.798 in 152,022 control chromosomes in the GnomAD database, including 48,657 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 0.80 (48657 hom., cov: 31)
• Consequence: ARL15 NM_019087.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890

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]

ARL15 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.29).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.817 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARL15	NM_019087.3	c.462+28477A>G		intron_variant		ENST00000504924.6	NP_061960.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARL15	ENST00000504924.6	c.462+28477A>G		intron_variant		1	NM_019087.3	ENSP00000433427.1
ARL15	ENST00000502271.5	c.-76+28477A>G		intron_variant		1		ENSP00000473508.1
ARL15	ENST00000507646.2	c.462+28477A>G		intron_variant		5		ENSP00000432680.1
ARL15	ENST00000510591.6	n.535+28477A>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.797 AC: 121140 AN: 151904 Hom.: 48598 Cov.: 31

Gnomad AFR AF: 0.824

Gnomad AMI AF: 0.885

Gnomad AMR AF: 0.793

Gnomad ASJ AF: 0.819

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.833

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.804

Gnomad OTH AF: 0.795

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

GnomAD4 genome AF: 0.798 AC: 121257 AN: 152022 Hom.: 48657 Cov.: 31 AF XY: 0.796 AC XY: 59131 AN XY: 74314

Gnomad4 AFR AF: 0.824

Gnomad4 AMR AF: 0.794

Gnomad4 ASJ AF: 0.819

Gnomad4 EAS AF: 0.493

Gnomad4 SAS AF: 0.710

Gnomad4 FIN AF: 0.833

Gnomad4 NFE AF: 0.804

Gnomad4 OTH AF: 0.795

Alfa AF: 0.810 Hom.: 9915

Bravo AF: 0.794

Asia WGS AF: 0.597 AC: 2078 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.29
CADD	Benign	20
DANN	Benign	0.80

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: rs273218; hg19: chr5-53380555;