chr5-54157764-T-C

Position:

• chr5-54157764-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_019087.3(ARL15):​c.194-3125A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 152,136 control chromosomes in the GnomAD database, including 4,066 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 0.21 (4066 hom., cov: 32)
• Consequence: ARL15 NM_019087.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.752

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=-0.47).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARL15	NM_019087.3	c.194-3125A>G		intron_variant		ENST00000504924.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARL15	ENST00000504924.6	c.194-3125A>G		intron_variant		1	NM_019087.3	P1

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31829 AN: 152018 Hom.: 4055 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.682

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.209 AC: 31861 AN: 152136 Hom.: 4066 Cov.: 32 AF XY: 0.215 AC XY: 16004 AN XY: 74372

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.160

Gnomad4 EAS AF: 0.682

Gnomad4 SAS AF: 0.359

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.217

Alfa AF: 0.187 Hom.: 332

Bravo AF: 0.215

Asia WGS AF: 0.518 AC: 1798 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	13
DANN	Benign	0.61

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: rs277330; hg19: chr5-53453594;