rs2732703

Positions:

• chr17-46275856-T-G

Variant summary

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

The NM_001103154.2(ARL17B):​c.*22-438A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0978 in 142,284 control chromosomes in the GnomAD database, including 1 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 0.098 (1 hom., cov: 36)
• Consequence: ARL17B NM_001103154.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.30

Genes affected

ARL17B (HGNC:32387): (ADP ribosylation factor like GTPase 17B) Predicted to enable GTP binding activity. Predicted to be involved in intracellular protein transport and vesicle-mediated transport. Predicted to be located in Golgi apparatus. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

LRRC37A (HGNC:29069): (leucine rich repeat containing 37A) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ARL17B (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARL17B	NM_001103154.2	c.*22-438A>C		intron_variant			NP_001096624.1
LRRC37A	XM_047437205.1	c.102-23938T>G		intron_variant			XP_047293161.1
LOC124904014	XR_007065823.1	n.77-1453T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARL17B	ENST00000570618.5	c.*22-438A>C		intron_variant		2		ENSP00000459151.1
ARL17B	ENST00000705759.1	n.377-438A>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0979 AC: 13921 AN: 142186 Hom.: 1 Cov.: 36

Gnomad AFR AF: 0.0319

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0488

Gnomad FIN AF: 0.0385

Gnomad MID AF: 0.164

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.0978 AC: 13909 AN: 142284 Hom.: 1 Cov.: 36 AF XY: 0.0912 AC XY: 6373 AN XY: 69872

Gnomad4 AFR AF: 0.0318

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.171

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0486

Gnomad4 FIN AF: 0.0385

Gnomad4 NFE AF: 0.152

Gnomad4 OTH AF: 0.122

Alfa AF: 0.136 Hom.: 4

Asia WGS AF: 0.0290 AC: 102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	16
DANN	Benign	0.80

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2732703; hg19: chr17-44353222;