chr5-53916587-G-C

Variant names:

• chr5-53916587-G-C
• rs2042313
• NM_019087.3:c.463-29874C>G

Variant summary

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

The NM_019087.3(ARL15):​c.463-29874C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.938 in 152,254 control chromosomes in the GnomAD database, including 67,510 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 0.94 (67510 hom., cov: 31)
• Consequence: ARL15 NM_019087.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.460
• 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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.99 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARL15	NM_019087.3	c.463-29874C>G		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.463-29874C>G		intron_variant	Intron 4 of 4	1	NM_019087.3	ENSP00000433427.1
ARL15	ENST00000502271.5	c.-75-29874C>G		intron_variant	Intron 4 of 4	1		ENSP00000473508.1
ARL15	ENST00000507646.2	c.463-29204C>G		intron_variant	Intron 4 of 4	5		ENSP00000432680.1
ARL15	ENST00000510591.6	n.536-29874C>G		intron_variant	Intron 4 of 4	5

Frequencies

GnomAD3 genomes AF: 0.938 AC: 142666 AN: 152136 Hom.: 67459 Cov.: 31

Gnomad AFR AF: 0.874

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.948

Gnomad ASJ AF: 0.984

Gnomad EAS AF: 0.647

Gnomad SAS AF: 0.783

Gnomad FIN AF: 0.984

Gnomad MID AF: 0.987

Gnomad NFE AF: 0.996

Gnomad OTH AF: 0.946

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

GnomAD4 genome AF: 0.938 AC: 142776 AN: 152254 Hom.: 67510 Cov.: 31 AF XY: 0.933 AC XY: 69438 AN XY: 74436

African (AFR) AF: 0.874 AC: 36326 AN: 41540

American (AMR) AF: 0.948 AC: 14487 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.984 AC: 3415 AN: 3470

East Asian (EAS) AF: 0.648 AC: 3358 AN: 5180

South Asian (SAS) AF: 0.783 AC: 3777 AN: 4822

European-Finnish (FIN) AF: 0.984 AC: 10443 AN: 10608

Middle Eastern (MID) AF: 0.986 AC: 290 AN: 294

European-Non Finnish (NFE) AF: 0.996 AC: 67774 AN: 68026

Other (OTH) AF: 0.943 AC: 1996 AN: 2116

Alfa AF: 0.966 Hom.: 7822

Bravo AF: 0.935

Asia WGS AF: 0.745 AC: 2596 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.53
DANN	Benign	0.57
PhyloP100		-0.46
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: rs2042313; hg19: chr5-53212417;