NM_001103154.2:c.*1120G>A

Variant names:

• chr17-46274320-C-T
• rs2732706
• NM_001103154.2:c.*1120G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001103154.2(ARL17B):​c.*1120G>A 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 151,958 control chromosomes in the GnomAD database, including 1,893 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 (1893 hom., cov: 36)
• Consequence: ARL17B NM_001103154.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.26
• Publications: 21 publications found

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]

ENSG00000305133 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• 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 rank	MANE	Protein	UniProt
ARL17B	NM_001103154.2	c.*1120G>A		3_prime_UTR_variant	Exon 5 of 5		NP_001096624.1
LRRC37A	XM_047437205.1	c.102-25474C>T		intron_variant	Intron 1 of 13		XP_047293161.1
LOC124904014	XR_007065823.1	n.76+229C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARL17B	ENST00000570618.6	c.*1120G>A		3_prime_UTR_variant	Exon 5 of 5	2		ENSP00000459151.1
ENSG00000305133	ENST00000809003.1	n.304+229C>T		intron_variant	Intron 4 of 7

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21742 AN: 151840 Hom.: 1895 Cov.: 36

Gnomad AFR AF: 0.0435

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0732

Gnomad FIN AF: 0.0655

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: 21731 AN: 151958 Hom.: 1893 Cov.: 36 AF XY: 0.134 AC XY: 9938 AN XY: 74282

African (AFR) AF: 0.0434 AC: 1800 AN: 41500

American (AMR) AF: 0.176 AC: 2677 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 816 AN: 3460

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5190

South Asian (SAS) AF: 0.0732 AC: 352 AN: 4808

European-Finnish (FIN) AF: 0.0655 AC: 694 AN: 10590

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.216 AC: 14668 AN: 67864

Other (OTH) AF: 0.180 AC: 379 AN: 2106

Alfa AF: 0.174 Hom.: 1245

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	-0.66
CADD	Benign	16
DANN	Benign	0.31
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs2732706; hg19: chr17-44351686;