NM_019087.3:c.48+31317T>A

Variant names:

• chr5-54279115-A-T
• rs3776649
• NM_019087.3:c.48+31317T>A

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+31317T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.572 in 152,062 control chromosomes in the GnomAD database, including 26,582 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 0.57 (26582 hom., cov: 32)
• Consequence: ARL15 NM_019087.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.582
• 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=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARL15	NM_019087.3	c.48+31317T>A		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+31317T>A		intron_variant	Intron 1 of 4	1	NM_019087.3	ENSP00000433427.1

Frequencies

GnomAD3 genomes AF: 0.572 AC: 86885 AN: 151946 Hom.: 26563 Cov.: 32

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.723

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.697

Gnomad EAS AF: 0.419

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.712

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.572 AC: 86927 AN: 152062 Hom.: 26582 Cov.: 32 AF XY: 0.569 AC XY: 42289 AN XY: 74336

African (AFR) AF: 0.369 AC: 15290 AN: 41458

American (AMR) AF: 0.488 AC: 7450 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.697 AC: 2419 AN: 3472

East Asian (EAS) AF: 0.419 AC: 2168 AN: 5174

South Asian (SAS) AF: 0.609 AC: 2940 AN: 4830

European-Finnish (FIN) AF: 0.712 AC: 7506 AN: 10548

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.693 AC: 47109 AN: 67992

Other (OTH) AF: 0.583 AC: 1232 AN: 2112

Alfa AF: 0.627 Hom.: 3866

Bravo AF: 0.545

Asia WGS AF: 0.512 AC: 1778 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.74
DANN	Benign	0.63
PhyloP100		-0.58
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: rs3776649; hg19: chr5-53574945; COSMIC: COSV72289964;