Genetic Variant ARL16:c.-3G>C (chr17-81683756-C-G) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001040025.3(ARL16):c.-3G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)

Consequence

ARL16
NM_001040025.3 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.685

Publications

0 publications found

Variant links:

Genes affected

ARL16 (HGNC:27902): (ADP ribosylation factor like GTPase 16) The protein encoded by this gene belongs to the ARL (ADP-ribosylation factor-like) family of proteins, which are structurally related to ADP-ribosylation factors (ARFs). This protein has been shown to have an inhibitory role in the cellular antiviral response. This gene product interacts with the C-terminal domain of the DEXD/H-box helicase 58 (DDX58) gene product. This interaction was found to suppress the association between the DDX58 gene product and RNA, thereby negatively regulating the activity of the DDX58 gene product. [provided by RefSeq, Jul 2016]

ARL16 links:

HGS (HGNC:4897): (hepatocyte growth factor-regulated tyrosine kinase substrate) The protein encoded by this gene regulates endosomal sorting and plays a critical role in the recycling and degradation of membrane receptors. The encoded protein sorts monoubiquitinated membrane proteins into the multivesicular body, targeting these proteins for lysosome-dependent degradation. [provided by RefSeq, Dec 2010]

HGS links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.18607661).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001040025.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ARL16	NM_001040025.3	MANE Select	c.-3G>C	5_prime_UTR	Exon 1 of 5	NP_001035114.2	B4E3H0
ARL16	NM_001329608.2		c.-670G>C	5_prime_UTR	Exon 1 of 5	NP_001316537.1
ARL16	NM_001329609.2		c.-230G>C	5_prime_UTR	Exon 1 of 4	NP_001316538.1	I3L4Z7

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ARL16	ENST00000622299.5	TSL:1 MANE Select	c.-3G>C	5_prime_UTR	Exon 1 of 5	ENSP00000483183.1	B4E3H0
HGS	ENST00000677161.1		c.-165+128C>G	intron	N/A	ENSP00000503695.1	A0A7I2V3Z1
ARL16	ENST00000577142.1	TSL:2	n.26G>C	non_coding_transcript_exon	Exon 1 of 3

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Cov.:

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

Bravo

AF:

0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.26

BayesDel_addAF

Benign

-0.080

BayesDel_noAF

Benign

-0.35

CADD

Benign

8.1

(source)

DANN

Benign

0.96

DEOGEN2

Benign

0.0021

Eigen

Benign

-0.77

Eigen_PC

Benign

-0.85

FATHMM_MKL

Benign

0.25

LIST_S2

Benign

0.41

M_CAP

Uncertain

0.28

MetaRNN

Benign

0.19

MetaSVM

Benign

-0.89

MutationAssessor

Benign

0.79

PhyloP100

-0.69

PrimateAI

Uncertain

0.71

PROVEAN

Benign

0.65

REVEL

Benign

0.073

Sift

Uncertain

0.0050

Sift4G

Uncertain

0.025

Polyphen

0.12

Vest4

0.22

MutPred

0.64

Gain of MoRF binding (P = 0.0174)

MVP

0.58

MPC

0.070

ClinPred

0.17

GERP RS

1.4

PromoterAI

-0.065

Neutral

(source)

Varity_R

0.15

gMVP

0.44

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over