rs10513040

Variant names:

• chr5-54206465-G-A
• rs10513040
• NM_019087.3:c.49-34537C>T

Variant summary

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

The NM_019087.3(ARL15):​c.49-34537C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0391 in 152,236 control chromosomes in the GnomAD database, including 185 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 0.039 (185 hom., cov: 32)
• Consequence: ARL15 NM_019087.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.120
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.13 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARL15	NM_019087.3	c.49-34537C>T		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.49-34537C>T		intron_variant	Intron 1 of 4	1	NM_019087.3	ENSP00000433427.1

Frequencies

GnomAD3 genomes AF: 0.0390 AC: 5939 AN: 152116 Hom.: 183 Cov.: 32

Gnomad AFR AF: 0.0105

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.0427

Gnomad ASJ AF: 0.0484

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.0893

Gnomad FIN AF: 0.0138

Gnomad MID AF: 0.0924

Gnomad NFE AF: 0.0457

Gnomad OTH AF: 0.0482

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

GnomAD4 genome AF: 0.0391 AC: 5945 AN: 152236 Hom.: 185 Cov.: 32 AF XY: 0.0403 AC XY: 2999 AN XY: 74428

African (AFR) AF: 0.0105 AC: 434 AN: 41524

American (AMR) AF: 0.0426 AC: 651 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0484 AC: 168 AN: 3472

East Asian (EAS) AF: 0.139 AC: 716 AN: 5166

South Asian (SAS) AF: 0.0906 AC: 437 AN: 4824

European-Finnish (FIN) AF: 0.0138 AC: 147 AN: 10620

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0458 AC: 3112 AN: 68014

Other (OTH) AF: 0.0477 AC: 101 AN: 2116

Alfa AF: 0.0459 Hom.: 99

Bravo AF: 0.0392

Asia WGS AF: 0.0880 AC: 307 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.51
PhyloP100		-0.12
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: rs10513040; hg19: chr5-53502295;