rs174345
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001290047.2(CECR2):c.*659A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.454 in 151,864 control chromosomes in the GnomAD database, including 16,058 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 0.45 ( 16058 hom., cov: 31)
Exomes 𝑓: 0.53 ( 20 hom. )
Failed GnomAD Quality Control
Consequence
CECR2
NM_001290047.2 3_prime_UTR
NM_001290047.2 3_prime_UTR
Scores
1
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.693
Genes affected
CECR2 (HGNC:1840): (CECR2 histone acetyl-lysine reader) This gene encodes a bromodomain-containing protein that is involved in chromatin remodeling, and may additionally play a role in DNA damage response. The encoded protein functions as part of an ATP-dependent complex that is involved in neurulation. This gene is a candidate gene for Cat Eye Syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2014]
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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=-0.88).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.537 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CECR2 | NM_001290047.2 | c.*659A>G | 3_prime_UTR_variant | 19/19 | ENST00000262608.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CECR2 | ENST00000262608.13 | c.*659A>G | 3_prime_UTR_variant | 19/19 | 1 | NM_001290047.2 | P2 | ||
ENST00000651475.1 | n.102-7448T>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.454 AC: 68848AN: 151746Hom.: 16063 Cov.: 31
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.530 AC: 70AN: 132Hom.: 20 Cov.: 0 AF XY: 0.565 AC XY: 52AN XY: 92
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Data not reliable, filtered out with message: AS_VQSR
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GnomAD4 genome ? AF: 0.454 AC: 68877AN: 151864Hom.: 16058 Cov.: 31 AF XY: 0.455 AC XY: 33755AN XY: 74214
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ClinVar
Not reported inComputational scores
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Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at