rs11894651
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001351368.2(C2orf92):c.665+4C>A variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.681 in 398,672 control chromosomes in the GnomAD database, including 95,255 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 0.68 ( 36398 hom., cov: 32)
Exomes 𝑓: 0.68 ( 58857 hom. )
Consequence
C2orf92
NM_001351368.2 splice_donor_region, intron
NM_001351368.2 splice_donor_region, intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.00
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=-0.51).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.729 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
C2orf92 | NM_001351368.2 | c.665+4C>A | splice_donor_region_variant, intron_variant | ENST00000627399.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C2orf92 | ENST00000627399.4 | c.665+4C>A | splice_donor_region_variant, intron_variant | 5 | NM_001351368.2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.683 AC: 103751AN: 151954Hom.: 36376 Cov.: 32
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GnomAD4 exome AF: 0.679 AC: 167556AN: 246600Hom.: 58857 Cov.: 0 AF XY: 0.679 AC XY: 84933AN XY: 125000
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GnomAD4 genome ? AF: 0.683 AC: 103821AN: 152072Hom.: 36398 Cov.: 32 AF XY: 0.675 AC XY: 50140AN XY: 74314
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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