3-93980726-AGTGT-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001174150.2(ARL13B):c.59+276_59+279del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.046 (210 hom., cov: 0)
• Consequence: ARL13B NM_001174150.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 2.30

Genes affected

ARL13B (HGNC:25419): (ADP ribosylation factor like GTPase 13B) This gene encodes a member of the ADP-ribosylation factor-like family. The encoded protein is a small GTPase that contains both N-terminal and C-terminal guanine nucleotide-binding motifs. This protein is localized in the cilia and plays a role in cilia formation and in maintenance of cilia. Mutations in this gene are the cause of Joubert syndrome 8. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Mar 2010]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 3-93980726-AGTGT-A is Benign according to our data. Variant chr3-93980726-AGTGT-A is described in ClinVar as [Benign]. Clinvar id is 1244366.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.08 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARL13B	NM_001174150.2	c.59+276_59+279del		intron_variant		ENST00000394222.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARL13B	ENST00000394222.8	c.59+276_59+279del		intron_variant		1	NM_001174150.2	P1

Frequencies

GnomAD3 genomes AF: 0.0462 AC: 6792 AN: 146908 Hom.: 210 Cov.: 0

Gnomad AFR AF: 0.0824

Gnomad AMI AF: 0.00114

Gnomad AMR AF: 0.0319

Gnomad ASJ AF: 0.0115

Gnomad EAS AF: 0.00581

Gnomad SAS AF: 0.0226

Gnomad FIN AF: 0.00957

Gnomad MID AF: 0.0162

Gnomad NFE AF: 0.0403

Gnomad OTH AF: 0.0388

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

GnomAD4 genome AF: 0.0463 AC: 6802 AN: 146990 Hom.: 210 Cov.: 0 AF XY: 0.0436 AC XY: 3124 AN XY: 71676

Gnomad4 AFR AF: 0.0824

Gnomad4 AMR AF: 0.0319

Gnomad4 ASJ AF: 0.0115

Gnomad4 EAS AF: 0.00583

Gnomad4 SAS AF: 0.0227

Gnomad4 FIN AF: 0.00957

Gnomad4 NFE AF: 0.0403

Gnomad4 OTH AF: 0.0400

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Oct 18, 2019

- -

Computational scores

Source: dbNSFP v4.3

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

LitVar

Other links and lift over

dbSNP: rs35756044; hg19: chr3-93699570;