dbSNP rs10510181: CHL1-AS2:n.208-33427C>T (chr3-149364-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 ENST00000663345.2(CHL1-AS2):n.208-33427C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 152,112 control chromosomes in the GnomAD database, including 8,207 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 0.31 ( 8207 hom., cov: 33)

Consequence

CHL1-AS2
ENST00000663345.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.648

Publications

18 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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.471 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	ENST00000663345.2 link	n.208-33427C>T	intron_variant	Intron 1 of 2
CHL1-AS2	ENST00000756999.1 link	n.254-33427C>T	intron_variant	Intron 1 of 2
CHL1-AS2	ENST00000757000.1 link	n.119-36904C>T	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.313

AC:

47607

AN:

151992

Hom.:

8203

Cov.:

show subpopulations

Gnomad AFR

AF:

0.193

Gnomad AMI

AF:

0.258

Gnomad AMR

AF:

0.382

Gnomad ASJ

AF:

0.247

Gnomad EAS

AF:

0.486

Gnomad SAS

AF:

0.243

Gnomad FIN

AF:

0.432

Gnomad MID

AF:

0.297

Gnomad NFE

AF:

0.348

Gnomad OTH

AF:

0.321

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

GnomAD4 genome

AF:

0.313

AC:

47632

AN:

152112

Hom.:

8207

Cov.:

AF XY:

0.318

AC XY:

23637

AN XY:

74356

show subpopulations

African (AFR)

AF:

0.193

AC:

8009

AN:

41520

American (AMR)

AF:

0.382

AC:

5840

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.247

AC:

857

AN:

3472

East Asian (EAS)

AF:

0.486

AC:

2514

AN:

5168

South Asian (SAS)

AF:

0.243

AC:

1173

AN:

4820

European-Finnish (FIN)

AF:

0.432

AC:

4563

AN:

10554

Middle Eastern (MID)

AF:

0.323

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.348

AC:

23670

AN:

67984

Other (OTH)

AF:

0.320

AC:

676

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1656

3313

4969

6626

8282

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

474

948

1422

1896

2370

<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:

0.330

Hom.:

28679

Bravo

AF:

0.303

Asia WGS

AF:

0.312

AC:

1082

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

7.1

(source)

DANN

Benign

0.72

PhyloP100

0.65

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