rs1400180
Positions:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000663345.1(CHL1-AS2):n.116-13348A>G variant causes a intron, non coding transcript 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)
Consequence
CHL1-AS2
ENST00000663345.1 intron, non_coding_transcript
ENST00000663345.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.619
Genes affected
CHL1-AS2 (HGNC:40147): (CHL1 antisense RNA 2)
Genome browser will be placed here
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=-0.62).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC107986057 | XR_001740582.2 | n.310+887T>C | intron_variant, non_coding_transcript_variant | ||||
LOC107986057 | XR_001740581.1 | n.311-321T>C | intron_variant, non_coding_transcript_variant | ||||
LOC107986057 | XR_001740583.1 | n.340-321T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHL1-AS2 | ENST00000663345.1 | n.116-13348A>G | intron_variant, non_coding_transcript_variant | ||||||
ENST00000671279.1 | n.153-321T>C | intron_variant, non_coding_transcript_variant | |||||||
CHL1-AS2 | ENST00000657108.1 | n.150+1911A>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
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