rs9754552

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000663345.1(CHL1-AS2):​n.116-32791T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.448 in 151,986 control chromosomes in the GnomAD database, including 16,297 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 0.45 ( 16297 hom., cov: 32)

Consequence

CHL1-AS2
ENST00000663345.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.578
Variant links:
Genes affected
CHL1-AS2 (HGNC:40147): (CHL1 antisense RNA 2)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CHL1-AS2ENST00000663345.1 linkuse as main transcriptn.116-32791T>C intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.448
AC:
68100
AN:
151868
Hom.:
16290
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.354
Gnomad AMI
AF:
0.595
Gnomad AMR
AF:
0.399
Gnomad ASJ
AF:
0.622
Gnomad EAS
AF:
0.0609
Gnomad SAS
AF:
0.428
Gnomad FIN
AF:
0.426
Gnomad MID
AF:
0.615
Gnomad NFE
AF:
0.539
Gnomad OTH
AF:
0.476
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.448
AC:
68145
AN:
151986
Hom.:
16297
Cov.:
32
AF XY:
0.442
AC XY:
32820
AN XY:
74266
show subpopulations
Gnomad4 AFR
AF:
0.354
Gnomad4 AMR
AF:
0.399
Gnomad4 ASJ
AF:
0.622
Gnomad4 EAS
AF:
0.0608
Gnomad4 SAS
AF:
0.429
Gnomad4 FIN
AF:
0.426
Gnomad4 NFE
AF:
0.539
Gnomad4 OTH
AF:
0.477
Alfa
AF:
0.357
Hom.:
1285
Bravo
AF:
0.444
Asia WGS
AF:
0.270
AC:
943
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
0.79
DANN
Benign
0.20

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs9754552; hg19: chr3-190411; API