chr3-93980428-T-G
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS1
The NM_001174150.2(ARL13B):c.5T>G(p.Phe2Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000143 in 1,612,562 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. F2F) has been classified as Likely benign.
Frequency
Consequence
NM_001174150.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARL13B | NM_001174150.2 | c.5T>G | p.Phe2Cys | missense_variant | 1/10 | ENST00000394222.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARL13B | ENST00000394222.8 | c.5T>G | p.Phe2Cys | missense_variant | 1/10 | 1 | NM_001174150.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000105 AC: 16AN: 152108Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000314 AC: 78AN: 248614Hom.: 0 AF XY: 0.000394 AC XY: 53AN XY: 134644
GnomAD4 exome AF: 0.000147 AC: 215AN: 1460336Hom.: 2 Cov.: 31 AF XY: 0.000213 AC XY: 155AN XY: 726614
GnomAD4 genome ? AF: 0.000105 AC: 16AN: 152226Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74420
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Jul 01, 2019 | In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Has not been previously published as pathogenic or benign to our knowledge - |
Joubert syndrome 8 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 16, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at