rs29911
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001145678.3(KIAA0825):c.2662+32G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 1,532,666 control chromosomes in the GnomAD database, including 11,594 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 0.12 ( 1191 hom., cov: 33)
Exomes 𝑓: 0.12 ( 10403 hom. )
Consequence
KIAA0825
NM_001145678.3 intron
NM_001145678.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0600
Genes affected
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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=-0.85).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.252 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIAA0825 | NM_001145678.3 | c.2662+32G>A | intron_variant | ENST00000682413.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIAA0825 | ENST00000682413.1 | c.2662+32G>A | intron_variant | NM_001145678.3 | A1 | ||||
KIAA0825 | ENST00000504117.1 | n.1556G>A | non_coding_transcript_exon_variant | 9/9 | 1 | ||||
KIAA0825 | ENST00000513200.7 | c.2662+32G>A | intron_variant | 5 | A1 | ||||
KIAA0825 | ENST00000703867.1 | c.2677+32G>A | intron_variant | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.117 AC: 17753AN: 151946Hom.: 1189 Cov.: 33
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GnomAD3 exomes AF: 0.132 AC: 20485AN: 154804Hom.: 1587 AF XY: 0.132 AC XY: 10799AN XY: 82100
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GnomAD4 exome AF: 0.117 AC: 161203AN: 1380604Hom.: 10403 Cov.: 26 AF XY: 0.117 AC XY: 79926AN XY: 681974
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GnomAD4 genome ? AF: 0.117 AC: 17767AN: 152062Hom.: 1191 Cov.: 33 AF XY: 0.120 AC XY: 8898AN XY: 74306
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at