rs1286731987
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001174150.2(ARL13B):c.1025-17T>C variant causes a intron 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. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
ARL13B
NM_001174150.2 intron
NM_001174150.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.92
Publications
0 publications found
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]
DHFR2 (HGNC:27309): (dihydrofolate reductase 2) Enables dihydrofolate reductase activity and mRNA binding activity. Involved in tetrahydrofolate metabolic process and thymidine biosynthetic process. Located in mitochondrial inner membrane and mitochondrial matrix. [provided by Alliance of Genome Resources, Apr 2022]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
Variant 3-94049389-T-C is Benign according to our data. Variant chr3-94049389-T-C is described in ClinVar as Likely_benign. ClinVar VariationId is 510717.Status of the report is criteria_provided_single_submitter, 1 stars.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001174150.2. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| ARL13B | TSL:1 MANE Select | c.1025-17T>C | intron | N/A | ENSP00000377769.3 | Q3SXY8-1 | |||
| ARL13B | TSL:1 | c.1025-17T>C | intron | N/A | ENSP00000420780.1 | Q3SXY8-1 | |||
| ARL13B | TSL:1 | c.716-17T>C | intron | N/A | ENSP00000445145.1 | Q3SXY8-3 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1330274Hom.: 0 Cov.: 19 AF XY: 0.00 AC XY: 0AN XY: 667926
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1330274
Hom.:
Cov.:
19
AF XY:
AC XY:
0
AN XY:
667926
African (AFR)
AF:
AC:
0
AN:
30270
American (AMR)
AF:
AC:
0
AN:
42282
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
24906
East Asian (EAS)
AF:
AC:
0
AN:
38860
South Asian (SAS)
AF:
AC:
0
AN:
79466
European-Finnish (FIN)
AF:
AC:
0
AN:
52922
Middle Eastern (MID)
AF:
AC:
0
AN:
5464
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1000342
Other (OTH)
AF:
AC:
0
AN:
55762
GnomAD4 genome
GnomAD4 genome
Cov.:
32
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
ClinVar submissions
View on ClinVar Significance:Likely benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
not specified (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.