rs12098599

chr10-18677031-G-T

Variant summary

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

The NM_178815.5(ARL5B):c.*1815G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 151,964 control chromosomes in the GnomAD database, including 3,575 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 (3566 hom., cov: 32)
  • Exomes 𝑓: 0.19 (9 hom.)
• Consequence: ARL5B NM_178815.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.311

Genes affected

ARL5B (HGNC:23052): (ADP ribosylation factor like GTPase 5B) ARL5B (ARL8) belongs to a family of proteins that are structurally similar to ADP-ribosylation factors (ARFs; see MIM 103180). ARLs and ARFs are part of the RAS superfamily of regulatory GTPases.[supplied by OMIM, Nov 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARL5B	NM_178815.5	c.*1815G>T		3_prime_UTR_variant	6/6	ENST00000377275.4
ARL5B	XM_005252400.2	c.*1815G>T		3_prime_UTR_variant	5/5
ARL5B	XM_005252401.5	c.*1815G>T		3_prime_UTR_variant	6/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARL5B	ENST00000377275.4	c.*1815G>T		3_prime_UTR_variant	6/6	1	NM_178815.5	P1

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31406 AN: 151410 Hom.: 3561 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.199

GnomAD4 exome AF: 0.189 AC: 83 AN: 438 Hom.: 9 Cov.: 0 AF XY: 0.189 AC XY: 50 AN XY: 264

Gnomad4 FIN exome AF: 0.190

Gnomad4 NFE exome AF: 0.125

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.208 AC: 31447 AN: 151526 Hom.: 3566 Cov.: 32 AF XY: 0.212 AC XY: 15727 AN XY: 74042

Gnomad4 AFR AF: 0.239

Gnomad4 AMR AF: 0.290

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.227

Gnomad4 SAS AF: 0.311

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.197

Alfa AF: 0.186 Hom.: 564

Bravo AF: 0.211

Asia WGS AF: 0.320 AC: 1113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	1.0
Dann	Benign	0.60
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.2

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: rs12098599; hg19: chr10-18965960; COSMIC: COSV66011154;