rs3737728
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_017891.5(C1orf159):c.311-23T>G variant causes a intron 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: 36)
Consequence
C1orf159
NM_017891.5 intron
NM_017891.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.27
Genes affected
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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=-0.87).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
C1orf159 | NM_017891.5 | c.311-23T>G | intron_variant | ENST00000421241.7 | |||
C1orf159 | NM_001330306.2 | c.419-23T>G | intron_variant | ||||
C1orf159 | NM_001363525.2 | c.311-23T>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C1orf159 | ENST00000421241.7 | c.311-23T>G | intron_variant | 2 | NM_017891.5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 36
GnomAD3 genomes
?
Cov.:
36
GnomAD4 exome Cov.: 51
GnomAD4 exome
Cov.:
51
GnomAD4 genome ? Cov.: 36
GnomAD4 genome
?
Cov.:
36
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at