rs7756167
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001134831.2(AHI1):c.3427-1309T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 985,342 control chromosomes in the GnomAD database, including 16,306 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.24 ( 9963 hom., cov: 33)
Exomes 𝑓: 0.083 ( 6343 hom. )
Consequence
AHI1
NM_001134831.2 intron
NM_001134831.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.15
Genes affected
AHI1 (HGNC:21575): (Abelson helper integration site 1) This gene is apparently required for both cerebellar and cortical development in humans. This gene mutations cause specific forms of Joubert syndrome-related disorders. Joubert syndrome (JS) is a recessively inherited developmental brain disorder with several identified causative chromosomal loci. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Oct 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.667 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AHI1 | NM_001134831.2 | c.3427-1309T>C | intron_variant | ENST00000265602.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AHI1 | ENST00000265602.11 | c.3427-1309T>C | intron_variant | 1 | NM_001134831.2 | P2 | |||
ENST00000444302.1 | n.123+177A>G | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.239 AC: 36371AN: 152164Hom.: 9922 Cov.: 33
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GnomAD4 exome AF: 0.0826 AC: 68822AN: 833060Hom.: 6343 Cov.: 31 AF XY: 0.0816 AC XY: 31379AN XY: 384694
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GnomAD4 genome ? AF: 0.240 AC: 36473AN: 152282Hom.: 9963 Cov.: 33 AF XY: 0.231 AC XY: 17226AN XY: 74474
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at