rs702634

Variant names:

• chr5-53975590-G-A
• rs702634
• NM_019087.3:c.463-88877C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-53975590-G-A
• chr5-53975590-G-C
• chr5-53975590-G-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.463-88877C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.721 in 152,188 control chromosomes in the GnomAD database, including 39,848 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 (39848 hom., cov: 33)
• Consequence: ARL15 NM_019087.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.264
• Publications: 72 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.838 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARL15	NM_019087.3	c.463-88877C>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.463-88877C>T		intron_variant	Intron 4 of 4	1	NM_019087.3	ENSP00000433427.1
ARL15	ENST00000502271.5	c.-75-88877C>T		intron_variant	Intron 4 of 4	1		ENSP00000473508.1
ARL15	ENST00000507646.2	c.463-88207C>T		intron_variant	Intron 4 of 4	5		ENSP00000432680.1
ARL15	ENST00000510591.6	n.536-88877C>T		intron_variant	Intron 4 of 4	5

Frequencies

GnomAD3 genomes AF: 0.721 AC: 109678 AN: 152070 Hom.: 39795 Cov.: 33

Gnomad AFR AF: 0.748

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.788

Gnomad ASJ AF: 0.712

Gnomad EAS AF: 0.859

Gnomad SAS AF: 0.753

Gnomad FIN AF: 0.645

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.691

Gnomad OTH AF: 0.734

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

GnomAD4 genome AF: 0.721 AC: 109783 AN: 152188 Hom.: 39848 Cov.: 33 AF XY: 0.721 AC XY: 53659 AN XY: 74388

African (AFR) AF: 0.748 AC: 31074 AN: 41526

American (AMR) AF: 0.789 AC: 12066 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.712 AC: 2471 AN: 3472

East Asian (EAS) AF: 0.859 AC: 4449 AN: 5178

South Asian (SAS) AF: 0.754 AC: 3635 AN: 4824

European-Finnish (FIN) AF: 0.645 AC: 6833 AN: 10588

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.691 AC: 46968 AN: 67982

Other (OTH) AF: 0.729 AC: 1541 AN: 2114

Alfa AF: 0.705 Hom.: 152177

Bravo AF: 0.733

Asia WGS AF: 0.783 AC: 2723 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.2
DANN	Benign	0.67
PhyloP100		0.26
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: rs702634; hg19: chr5-53271420;