5-54151696-G-A

Variant names:

• chr5-54151696-G-A
• rs157069
• NM_019087.3:c.253+2884C>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.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
• Publications: 2 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_019087.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARL15	NM_019087.3	MANE Select	c.253+2884C>T		intron	N/A	NP_061960.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARL15	ENST00000504924.6	TSL:1 MANE Select	c.253+2884C>T		intron	N/A	ENSP00000433427.1
	ARL15	ENST00000502271.5	TSL:1	c.-285+2884C>T		intron	N/A	ENSP00000473508.1
	ARL15	ENST00000505630.5	TSL:1	n.350+2884C>T		intron	N/A

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

African (AFR) AF: 0.203 AC: 8411 AN: 41464

American (AMR) AF: 0.223 AC: 3405 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 556 AN: 3468

East Asian (EAS) AF: 0.683 AC: 3520 AN: 5150

South Asian (SAS) AF: 0.359 AC: 1726 AN: 4810

European-Finnish (FIN) AF: 0.155 AC: 1638 AN: 10538

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.176 AC: 11955 AN: 67884

Other (OTH) AF: 0.216 AC: 454 AN: 2106

Alfa AF: 0.187 Hom.: 294

Bravo AF: 0.214

Asia WGS AF: 0.517 AC: 1792 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.0
DANN	Benign	0.63
PhyloP100		-0.044
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: rs157069; hg19: chr5-53447526;