rs6450176

Variant names:

• chr5-54002195-G-A
• rs6450176
• NM_019087.3:c.462+111007C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-54002195-G-A
• chr5-54002195-G-C

Variant summary

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

The NM_019087.3(ARL15):​c.462+111007C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 152,044 control chromosomes in the GnomAD database, including 6,032 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 0.28 (6032 hom., cov: 33)
• Consequence: ARL15 NM_019087.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.282
• Publications: 94 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=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARL15	NM_019087.3	c.462+111007C>T		intron_variant	Intron 4 of 4	ENST00000504924.6	NP_061960.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARL15	ENST00000504924.6	c.462+111007C>T		intron_variant	Intron 4 of 4	1	NM_019087.3	ENSP00000433427.1
ARL15	ENST00000502271.5	c.-76+111007C>T		intron_variant	Intron 4 of 4	1		ENSP00000473508.1
ARL15	ENST00000507646.2	c.462+111007C>T		intron_variant	Intron 4 of 4	5		ENSP00000432680.1
ARL15	ENST00000510591.6	n.535+111007C>T		intron_variant	Intron 4 of 4	5

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41908 AN: 151926 Hom.: 6026 Cov.: 33

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.276 AC: 41949 AN: 152044 Hom.: 6032 Cov.: 33 AF XY: 0.277 AC XY: 20560 AN XY: 74320

African (AFR) AF: 0.299 AC: 12385 AN: 41468

American (AMR) AF: 0.288 AC: 4393 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 692 AN: 3472

East Asian (EAS) AF: 0.457 AC: 2359 AN: 5160

South Asian (SAS) AF: 0.323 AC: 1555 AN: 4814

European-Finnish (FIN) AF: 0.239 AC: 2529 AN: 10590

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.253 AC: 17195 AN: 67970

Other (OTH) AF: 0.290 AC: 613 AN: 2112

Alfa AF: 0.264 Hom.: 22832

Bravo AF: 0.277

Asia WGS AF: 0.410 AC: 1422 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	14
DANN	Benign	0.63
PhyloP100		0.28
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: rs6450176; hg19: chr5-53298025; COSMIC: COSV72289494;