chr5-54015672-C-A

Variant names:

• chr5-54015672-C-A
• rs255758
• NM_019087.3:c.462+97530G>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.462+97530G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.718 in 151,988 control chromosomes in the GnomAD database, including 39,508 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 0.72 (39508 hom., cov: 31)
• Consequence: ARL15 NM_019087.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.531
• Publications: 16 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 (EAS) allele frequency at 95% confidence interval = 0.831 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARL15	NM_019087.3	c.462+97530G>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+97530G>T		intron_variant	Intron 4 of 4	1	NM_019087.3	ENSP00000433427.1
ARL15	ENST00000502271.5	c.-76+97530G>T		intron_variant	Intron 4 of 4	1		ENSP00000473508.1
ARL15	ENST00000507646.2	c.462+97530G>T		intron_variant	Intron 4 of 4	5		ENSP00000432680.1
ARL15	ENST00000510591.6	n.535+97530G>T		intron_variant	Intron 4 of 4	5

Frequencies

GnomAD3 genomes AF: 0.718 AC: 109099 AN: 151870 Hom.: 39471 Cov.: 31

Gnomad AFR AF: 0.635

Gnomad AMI AF: 0.653

Gnomad AMR AF: 0.801

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.852

Gnomad SAS AF: 0.760

Gnomad FIN AF: 0.727

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.737

Gnomad OTH AF: 0.727

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

GnomAD4 genome AF: 0.718 AC: 109187 AN: 151988 Hom.: 39508 Cov.: 31 AF XY: 0.719 AC XY: 53449 AN XY: 74292

African (AFR) AF: 0.635 AC: 26306 AN: 41416

American (AMR) AF: 0.801 AC: 12236 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.709 AC: 2461 AN: 3472

East Asian (EAS) AF: 0.852 AC: 4409 AN: 5176

South Asian (SAS) AF: 0.761 AC: 3661 AN: 4812

European-Finnish (FIN) AF: 0.727 AC: 7689 AN: 10570

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.737 AC: 50086 AN: 67960

Other (OTH) AF: 0.722 AC: 1522 AN: 2108

Alfa AF: 0.740 Hom.: 33016

Bravo AF: 0.722

Asia WGS AF: 0.780 AC: 2711 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.37
DANN	Benign	0.39
PhyloP100		-0.53
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: rs255758; hg19: chr5-53311502; COSMIC: COSV72289573;