rs968
Positions:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NR_026947.1(C1RL-AS1):n.2236T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
C1RL-AS1
NR_026947.1 non_coding_transcript_exon
NR_026947.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.428
Genes affected
C1RL-AS1 (HGNC:27461): (C1RL antisense RNA 1)
RBP5 (HGNC:15847): (retinol binding protein 5) The protein encoded by this gene is a cellular retinol-binding protein expressed highly in kidney and liver. Down-regulation of the encoded protein in hepatocellular carcinoma was associated with large tumor size and poor patient survival rates. [provided by RefSeq, Jul 2016]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
C1RL-AS1 | NR_026947.1 | n.2236T>C | non_coding_transcript_exon_variant | 8/12 | |||
RBP5 | XR_001748882.2 | n.1963A>G | non_coding_transcript_exon_variant | 6/6 | |||
RBP5 | XR_007063132.1 | n.2160A>G | non_coding_transcript_exon_variant | 6/6 | |||
RBP5 | XR_007063133.1 | n.2069A>G | non_coding_transcript_exon_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C1RL-AS1 | ENST00000541775.5 | n.2236T>C | non_coding_transcript_exon_variant | 8/12 | 1 | ||||
C1RL-AS1 | ENST00000535078.2 | n.307+864T>C | intron_variant, non_coding_transcript_variant | 2 | |||||
RBP5 | ENST00000619522.2 | n.2114A>G | non_coding_transcript_exon_variant | 4/4 | |||||
C1RL-AS1 | ENST00000382215.3 | n.1382+864T>C | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 18Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 14
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
18
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
14
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at