rs201148693
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_001134831.2(AHI1):c.3418C>T(p.Pro1140Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000602 in 1,584,320 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001134831.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AHI1 | NM_001134831.2 | c.3418C>T | p.Pro1140Ser | missense_variant | 26/29 | ENST00000265602.11 | NP_001128303.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AHI1 | ENST00000265602.11 | c.3418C>T | p.Pro1140Ser | missense_variant | 26/29 | 1 | NM_001134831.2 | ENSP00000265602.6 |
Frequencies
GnomAD3 genomes AF: 0.000335 AC: 51AN: 152142Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000453 AC: 95AN: 209548Hom.: 0 AF XY: 0.000481 AC XY: 54AN XY: 112336
GnomAD4 exome AF: 0.000631 AC: 904AN: 1432060Hom.: 1 Cov.: 30 AF XY: 0.000643 AC XY: 456AN XY: 709676
GnomAD4 genome AF: 0.000328 AC: 50AN: 152260Hom.: 0 Cov.: 32 AF XY: 0.000363 AC XY: 27AN XY: 74444
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Oct 25, 2021 | Reported in the heterozygous state in a parent of a child with JSRD, but did not segregate in the affected child and was concluded to be of unclear significance (Valente et al., 2006); In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 16453322) - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Joubert syndrome 3 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 28, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. - |
Intellectual disability Benign:1
Likely benign, no assertion criteria provided | clinical testing | Centre de Biologie Pathologie Génétique, Centre Hospitalier Universitaire de Lille | Jan 01, 2019 | - - |
Familial aplasia of the vermis Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at