chr5-53975590-G-A

Position:

• chr5-53975590-G-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
ARL15	NM_019087.3	c.463-88877C>T		intron_variant		ENST00000504924.6	NP_061960.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARL15	ENST00000504924.6	c.463-88877C>T		intron_variant		1	NM_019087.3	ENSP00000433427	P1
ARL15	ENST00000502271.5	c.-75-88877C>T		intron_variant		1		ENSP00000473508
ARL15	ENST00000507646.2	c.463-88207C>T		intron_variant		5		ENSP00000432680
ARL15	ENST00000510591.6	n.536-88877C>T		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.748

Gnomad4 AMR AF: 0.789

Gnomad4 ASJ AF: 0.712

Gnomad4 EAS AF: 0.859

Gnomad4 SAS AF: 0.754

Gnomad4 FIN AF: 0.645

Gnomad4 NFE AF: 0.691

Gnomad4 OTH AF: 0.729

Alfa AF: 0.701 Hom.: 61882

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs702634; hg19: chr5-53271420;