rs250387

Variant names:

• chr5-54288807-T-C
• rs250387
• NM_019087.3:c.48+21625A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_019087.3(ARL15):​c.48+21625A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.296 in 151,924 control chromosomes in the GnomAD database, including 7,656 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 0.30 (7656 hom., cov: 32)
• Consequence: ARL15 NM_019087.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.475 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARL15	NM_019087.3	c.48+21625A>G		intron_variant	Intron 1 of 4	ENST00000504924.6	NP_061960.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARL15	ENST00000504924.6	c.48+21625A>G		intron_variant	Intron 1 of 4	1	NM_019087.3	ENSP00000433427.1

Frequencies

GnomAD3 genomes AF: 0.296 AC: 44964 AN: 151806 Hom.: 7651 Cov.: 32

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.296 AC: 45005 AN: 151924 Hom.: 7656 Cov.: 32 AF XY: 0.294 AC XY: 21793 AN XY: 74206

African (AFR) AF: 0.481 AC: 19904 AN: 41390

American (AMR) AF: 0.239 AC: 3649 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 612 AN: 3462

East Asian (EAS) AF: 0.200 AC: 1038 AN: 5178

South Asian (SAS) AF: 0.163 AC: 782 AN: 4806

European-Finnish (FIN) AF: 0.226 AC: 2378 AN: 10536

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15712 AN: 67982

Other (OTH) AF: 0.290 AC: 610 AN: 2102

Alfa AF: 0.272 Hom.: 815

Bravo AF: 0.303

Asia WGS AF: 0.210 AC: 730 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.13
DANN	Benign	0.77
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs250387; hg19: chr5-53584637;