GeneBe

rs1400180

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B.

Score: -2 - Likely Benign
-2
-12 -7 -6 -1 0 5 6 9 10 12
PM2BP4_Strong

The ENST00000657108.2(CHL1-AS2):​n.156+1911A>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: 32)

Consequence

CHL1-AS2
ENST00000657108.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.619

Publications

5 publications found
Variant links:
Genes affected
CHL1-AS2 (HGNC:40147): (CHL1 antisense RNA 2)

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -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 rank MANE Protein UniProt
LOC107986057XR_001740581.1 linkn.311-321T>C intron_variant Intron 2 of 2
LOC107986057XR_001740582.2 linkn.310+887T>C intron_variant Intron 2 of 2
LOC107986057XR_001740583.1 linkn.340-321T>C intron_variant Intron 2 of 2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CHL1-AS2ENST00000657108.2 linkn.156+1911A>G intron_variant Intron 1 of 2
CHL1-AS2ENST00000663345.2 linkn.208-13348A>G intron_variant Intron 1 of 2
ENSG00000287140ENST00000671279.1 linkn.153-321T>C intron_variant Intron 1 of 1

Frequencies

GnomAD3 genomes
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.62
CADD
Benign
8.9
DANN
Benign
0.86
PhyloP100
0.62

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs1400180; hg19: chr3-170968; API