17-46274563-T-G

Position:

• chr17-46274563-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.*877A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 151,960 control chromosomes in the GnomAD database, including 1,892 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 (1892 hom., cov: 36)
• Consequence: ARL17B NM_001103154.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.80

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARL17B	NM_001103154.2	c.*877A>C		3_prime_UTR_variant	5/5		NP_001096624.1
LRRC37A	XM_047437205.1	c.102-25231T>G		intron_variant			XP_047293161.1
		n.46274563T>G		intergenic_region
LOC124904014	XR_007065823.1	n.76+472T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21734 AN: 151840 Hom.: 1894 Cov.: 36

Gnomad AFR AF: 0.0434

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0741

Gnomad FIN AF: 0.0654

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.143 AC: 21724 AN: 151960 Hom.: 1892 Cov.: 36 AF XY: 0.134 AC XY: 9935 AN XY: 74292

Gnomad4 AFR AF: 0.0433

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.00155

Gnomad4 SAS AF: 0.0741

Gnomad4 FIN AF: 0.0654

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.180

Alfa AF: 0.162 Hom.: 365

Bravo AF: 0.150

Asia WGS AF: 0.0310 AC: 109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	16
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2732705; hg19: chr17-44351929;