rs2668622

chr17-46274765-G-T

Variant summary

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

The XR_007065823.1(LOC124904014):n.76+674G>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 150,430 control chromosomes in the GnomAD database, including 1,921 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 0.14 (1915 hom., cov: 36)
  • Exomes 𝑓: 0.14 (6 hom.)
• Consequence: LOC124904014 XR_007065823.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.94

Genes affected

LOC124904014 (HGNC:):

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124904014	XR_007065823.1	n.76+674G>T		intron_variant, non_coding_transcript_variant
ARL17B	NM_001103154.2	c.*675C>A		3_prime_UTR_variant	5/5
LRRC37A	XM_047437205.1	c.102-25029G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARL17B	ENST00000570618.5			downstream_gene_variant		2

Frequencies

GnomAD3 genomes AF: 0.145 AC: 21705 AN: 149878 Hom.: 1917 Cov.: 36

Gnomad AFR AF: 0.0440

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.00157

Gnomad SAS AF: 0.0743

Gnomad FIN AF: 0.0677

Gnomad MID AF: 0.220

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.185

GnomAD4 exome AF: 0.144 AC: 66 AN: 458 Hom.: 6 Cov.: 0 AF XY: 0.161 AC XY: 47 AN XY: 292

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0984

Gnomad4 NFE exome AF: 0.359

Gnomad4 OTH exome AF: 0.125

GnomAD4 genome AF: 0.145 AC: 21693 AN: 149972 Hom.: 1915 Cov.: 36 AF XY: 0.136 AC XY: 9919 AN XY: 73150

Gnomad4 AFR AF: 0.0439

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.237

Gnomad4 EAS AF: 0.00157

Gnomad4 SAS AF: 0.0744

Gnomad4 FIN AF: 0.0677

Gnomad4 NFE AF: 0.217

Gnomad4 OTH AF: 0.182

Alfa AF: 0.191 Hom.: 979

Bravo AF: 0.151

Asia WGS AF: 0.0310 AC: 111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
Cadd	Benign	17
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2668622; hg19: chr17-44352131;