3-94003798-T-C
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_001174150.2(ARL13B):āc.270T>Cā(p.Tyr90=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000161 in 1,613,574 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Genomes: š 0.000066 ( 0 hom., cov: 32)
Exomes š: 0.000011 ( 0 hom. )
Consequence
ARL13B
NM_001174150.2 synonymous
NM_001174150.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.238
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.59).
BP6
Variant 3-94003798-T-C is Benign according to our data. Variant chr3-94003798-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 263013.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=0.238 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARL13B | NM_001174150.2 | c.270T>C | p.Tyr90= | synonymous_variant | 3/10 | ENST00000394222.8 | NP_001167621.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ARL13B | ENST00000394222.8 | c.270T>C | p.Tyr90= | synonymous_variant | 3/10 | 1 | NM_001174150.2 | ENSP00000377769 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000658 AC: 10AN: 152054Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251248Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135790
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GnomAD4 exome AF: 0.0000109 AC: 16AN: 1461520Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 727064
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GnomAD4 genome AF: 0.0000658 AC: 10AN: 152054Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74268
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Joubert syndrome 8 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jul 25, 2023 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at