rs12264028
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000373886.8(BICC1):c.190+5047C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.54 in 151,766 control chromosomes in the GnomAD database, including 23,205 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 0.54 ( 23205 hom., cov: 31)
Consequence
BICC1
ENST00000373886.8 intron
ENST00000373886.8 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.49
Genes affected
BICC1 (HGNC:19351): (BicC family RNA binding protein 1) This gene encodes an RNA-binding protein that is active in regulating gene expression by modulating protein translation during embryonic development. Mouse studies identified the corresponding protein to be under strict control during cell differentiation and to be a maternally provided gene product. [provided by RefSeq, Apr 2009]
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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 = 0.704 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BICC1 | NM_001080512.3 | c.190+5047C>T | intron_variant | ENST00000373886.8 | NP_001073981.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BICC1 | ENST00000373886.8 | c.190+5047C>T | intron_variant | 1 | NM_001080512.3 | ENSP00000362993 | P1 |
Frequencies
GnomAD3 genomes AF: 0.540 AC: 81901AN: 151648Hom.: 23154 Cov.: 31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.540 AC: 81995AN: 151766Hom.: 23205 Cov.: 31 AF XY: 0.541 AC XY: 40101AN XY: 74136
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1957
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at