rs11158569
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001386928.1(CHURC1):c.*1121C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 983,474 control chromosomes in the GnomAD database, including 23,993 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 0.26 ( 6084 hom., cov: 32)
Exomes 𝑓: 0.20 ( 17909 hom. )
Consequence
CHURC1
NM_001386928.1 3_prime_UTR
NM_001386928.1 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.583
Genes affected
CHURC1 (HGNC:20099): (churchill domain containing 1) Predicted to enable zinc ion binding activity. Predicted to be involved in positive regulation of transcription, DNA-templated. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.91).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHURC1 | NM_001386928.1 | c.*1121C>T | 3_prime_UTR_variant | 4/4 | ENST00000549115.7 | ||
CHURC1-FNTB | NM_001202559.1 | c.327+7271C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHURC1 | ENST00000549115.7 | c.*1121C>T | 3_prime_UTR_variant | 4/4 | 1 | NM_001386928.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.264 AC: 40151AN: 151952Hom.: 6059 Cov.: 32
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GnomAD4 exome AF: 0.204 AC: 169618AN: 831404Hom.: 17909 Cov.: 19 AF XY: 0.205 AC XY: 78699AN XY: 384034
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GnomAD4 genome ? AF: 0.265 AC: 40239AN: 152070Hom.: 6084 Cov.: 32 AF XY: 0.266 AC XY: 19784AN XY: 74348
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at