rs4240529
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_003928.2(CHIAP2):n.602A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.696 in 170,856 control chromosomes in the GnomAD database, including 42,184 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 0.70 ( 37652 hom., cov: 30)
Exomes 𝑓: 0.68 ( 4532 hom. )
Consequence
CHIAP2
NR_003928.2 non_coding_transcript_exon
NR_003928.2 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.356
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=-0.95).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.921 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHIAP2 | NR_003928.2 | n.602A>G | non_coding_transcript_exon_variant | 2/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHIAP2 | ENST00000369743.8 | n.628A>G | non_coding_transcript_exon_variant | 3/9 | 5 | ||||
CHIAP2 | ENST00000532686.5 | n.258-297A>G | intron_variant, non_coding_transcript_variant | ||||||
CHIAP2 | ENST00000456752.6 | n.336+261A>G | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.698 AC: 106025AN: 151792Hom.: 37641 Cov.: 30
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GnomAD4 exome AF: 0.680 AC: 12891AN: 18946Hom.: 4532 Cov.: 0 AF XY: 0.689 AC XY: 6695AN XY: 9722
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GnomAD4 genome ? AF: 0.698 AC: 106079AN: 151910Hom.: 37652 Cov.: 30 AF XY: 0.705 AC XY: 52332AN XY: 74242
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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