Variant 5-54310465-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6BP7BA1

The NM_019087.3(ARL15):c.15A>G(p.Arg5=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.838 in 1,607,190 control chromosomes in the GnomAD database, including 565,559 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.86 ( 56236 hom., cov: 32)

Exomes 𝑓: 0.84 ( 509323 hom. )

Consequence

ARL15
NM_019087.3 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.181

Variant links:

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]

ARL15 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.46).

BP6

Variant 5-54310465-T-C is Benign according to our data. Variant chr5-54310465-T-C is described in ClinVar as [Benign]. Clinvar id is 3060130.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr5-54310465-T-C is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=0.181 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARL15	NM_019087.3 linkuse as main transcript	c.15A>G	p.Arg5=	synonymous_variant	1/5	ENST00000504924.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARL15	ENST00000504924.6 linkuse as main transcript	c.15A>G	p.Arg5=	synonymous_variant	1/5	1	NM_019087.3	P1

Frequencies

GnomAD3 genomes

AF:

0.858

AC:

130404

AN:

152002

Hom.:

56185

Cov.:

show subpopulations

Gnomad AFR

AF:

0.930

Gnomad AMI

AF:

0.833

Gnomad AMR

AF:

0.809

Gnomad ASJ

AF:

0.754

Gnomad EAS

AF:

0.720

Gnomad SAS

AF:

0.797

Gnomad FIN

AF:

0.859

Gnomad MID

AF:

0.820

Gnomad NFE

AF:

0.846

Gnomad OTH

AF:

0.839

GnomAD3 exomes

AF:

0.817

AC:

192174

AN:

235304

Hom.:

78772

AF XY:

0.818

AC XY:

104443

AN XY:

127728

show subpopulations

Gnomad AFR exome

AF:

0.932

Gnomad AMR exome

AF:

0.759

Gnomad ASJ exome

AF:

0.757

Gnomad EAS exome

AF:

0.710

Gnomad SAS exome

AF:

0.791

Gnomad FIN exome

AF:

0.850

Gnomad NFE exome

AF:

0.843

Gnomad OTH exome

AF:

0.816

GnomAD4 exome

AF:

0.836

AC:

1216290

AN:

1455070

Hom.:

509323

Cov.:

AF XY:

0.835

AC XY:

603682

AN XY:

723038

show subpopulations

Gnomad4 AFR exome

AF:

0.932

Gnomad4 AMR exome

AF:

0.767

Gnomad4 ASJ exome

AF:

0.753

Gnomad4 EAS exome

AF:

0.720

Gnomad4 SAS exome

AF:

0.795

Gnomad4 FIN exome

AF:

0.852

Gnomad4 NFE exome

AF:

0.845

Gnomad4 OTH exome

AF:

0.827

GnomAD4 genome

AF:

0.858

AC:

130508

AN:

152120

Hom.:

56236

Cov.:

AF XY:

0.856

AC XY:

63665

AN XY:

74340

show subpopulations

Gnomad4 AFR

AF:

0.930

Gnomad4 AMR

AF:

0.809

Gnomad4 ASJ

AF:

0.754

Gnomad4 EAS

AF:

0.721

Gnomad4 SAS

AF:

0.798

Gnomad4 FIN

AF:

0.859

Gnomad4 NFE

AF:

0.846

Gnomad4 OTH

AF:

0.833

Alfa

AF:

0.843

Hom.:

72470

Bravo

AF:

0.855

Asia WGS

AF:

0.746

AC:

2593

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

ARL15-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 30, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.46

CADD

Benign

DANN

Benign

0.79

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over