rs4865796

Variant names:

• chr5-53976834-G-A
• rs4865796
• NM_019087.3:c.463-90121C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-53976834-G-A
• chr5-53976834-G-C
• chr5-53976834-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.463-90121C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.722 in 152,026 control chromosomes in the GnomAD database, including 39,887 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 (39887 hom., cov: 31)
• Consequence: ARL15 NM_019087.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0680
• Publications: 51 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.843 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_019087.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARL15	NM_019087.3	MANE Select	c.463-90121C>T		intron	N/A	NP_061960.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARL15	ENST00000504924.6	TSL:1 MANE Select	c.463-90121C>T		intron	N/A	ENSP00000433427.1
	ARL15	ENST00000502271.5	TSL:1	c.-75-90121C>T		intron	N/A	ENSP00000473508.1
	ARL15	ENST00000507646.2	TSL:5	c.463-89451C>T		intron	N/A	ENSP00000432680.1

Frequencies

GnomAD3 genomes AF: 0.722 AC: 109683 AN: 151908 Hom.: 39833 Cov.: 31

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.789

Gnomad ASJ AF: 0.711

Gnomad EAS AF: 0.864

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.753

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: 0.722 AC: 109789 AN: 152026 Hom.: 39887 Cov.: 31 AF XY: 0.722 AC XY: 53627 AN XY: 74298

African (AFR) AF: 0.751 AC: 31125 AN: 41438

American (AMR) AF: 0.789 AC: 12071 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.711 AC: 2463 AN: 3466

East Asian (EAS) AF: 0.864 AC: 4468 AN: 5170

South Asian (SAS) AF: 0.749 AC: 3610 AN: 4818

European-Finnish (FIN) AF: 0.644 AC: 6804 AN: 10564

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

European-Non Finnish (NFE) AF: 0.691 AC: 46966 AN: 67964

Other (OTH) AF: 0.729 AC: 1539 AN: 2112

Alfa AF: 0.712 Hom.: 52925

Bravo AF: 0.734

Asia WGS AF: 0.787 AC: 2738 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.61
DANN	Benign	0.76
PhyloP100		0.068
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: rs4865796; hg19: chr5-53272664;