dbSNP rs17033096: CHL1-AS2:n.157-1463C>T (chr3-117400-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000657108.2(CHL1-AS2):n.157-1463C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 151,816 control chromosomes in the GnomAD database, including 3,652 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 0.21 ( 3652 hom., cov: 32)

Consequence

CHL1-AS2
ENST00000657108.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0930

Publications

2 publications found

Variant links:

Genes affected

CHL1-AS2 (HGNC:40147): (CHL1 antisense RNA 2)

CHL1-AS2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
CHL1-AS2	ENST00000657108.2 link	n.157-1463C>T	intron_variant	Intron 1 of 2
CHL1-AS2	ENST00000663345.2 link	n.208-1463C>T	intron_variant	Intron 1 of 2
CHL1-AS2	ENST00000756999.1 link	n.254-1463C>T	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.209

AC:

31728

AN:

151700

Hom.:

3646

Cov.:

show subpopulations

Gnomad AFR

AF:

0.311

Gnomad AMI

AF:

0.215

Gnomad AMR

AF:

0.143

Gnomad ASJ

AF:

0.213

Gnomad EAS

AF:

0.0532

Gnomad SAS

AF:

0.233

Gnomad FIN

AF:

0.136

Gnomad MID

AF:

0.229

Gnomad NFE

AF:

0.184

Gnomad OTH

AF:

0.197

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.209

AC:

31778

AN:

151816

Hom.:

3652

Cov.:

AF XY:

0.207

AC XY:

15371

AN XY:

74208

show subpopulations

African (AFR)

AF:

0.311

AC:

12852

AN:

41266

American (AMR)

AF:

0.143

AC:

2184

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.213

AC:

740

AN:

3472

East Asian (EAS)

AF:

0.0533

AC:

276

AN:

5176

South Asian (SAS)

AF:

0.234

AC:

1122

AN:

4804

European-Finnish (FIN)

AF:

0.136

AC:

1431

AN:

10542

Middle Eastern (MID)

AF:

0.229

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.184

AC:

12486

AN:

67968

Other (OTH)

AF:

0.201

AC:

424

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1280

2560

3841

5121

6401

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

340

680

1020

1360

1700

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.185

Hom.:

3372

Bravo

AF:

0.212

Asia WGS

AF:

0.173

AC:

601

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

7.1

(source)

DANN

Benign

0.63

PhyloP100

0.093

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over