Genetic Variant CHL1-AS2:n.207+36256A>G (chr3-160351-T-C) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000663345.2(CHL1-AS2):n.207+36256A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 152,040 control chromosomes in the GnomAD database, including 15,946 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 ( 15946 hom., cov: 33)

Consequence

CHL1-AS2
ENST00000663345.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.309

Publications

5 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 -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.3).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.513 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.207+36256A>G	intron_variant	Intron 1 of 2
CHL1-AS2	ENST00000756999.1 link	n.253+36616A>G	intron_variant	Intron 1 of 2
CHL1-AS2	ENST00000757000.1 link	n.118+36256A>G	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.451

AC:

68456

AN:

151922

Hom.:

15950

Cov.:

show subpopulations

Gnomad AFR

AF:

0.519

Gnomad AMI

AF:

0.507

Gnomad AMR

AF:

0.390

Gnomad ASJ

AF:

0.490

Gnomad EAS

AF:

0.0992

Gnomad SAS

AF:

0.350

Gnomad FIN

AF:

0.392

Gnomad MID

AF:

0.563

Gnomad NFE

AF:

0.461

Gnomad OTH

AF:

0.468

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

GnomAD4 genome

AF:

0.450

AC:

68472

AN:

152040

Hom.:

15946

Cov.:

AF XY:

0.443

AC XY:

32948

AN XY:

74298

show subpopulations

African (AFR)

AF:

0.518

AC:

21517

AN:

41500

American (AMR)

AF:

0.390

AC:

5945

AN:

15254

Ashkenazi Jewish (ASJ)

AF:

0.490

AC:

1701

AN:

3470

East Asian (EAS)

AF:

0.0992

AC:

513

AN:

5170

South Asian (SAS)

AF:

0.350

AC:

1686

AN:

4818

European-Finnish (FIN)

AF:

0.392

AC:

4141

AN:

10558

Middle Eastern (MID)

AF:

0.554

AC:

163

AN:

294

European-Non Finnish (NFE)

AF:

0.461

AC:

31350

AN:

67952

Other (OTH)

AF:

0.471

AC:

994

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1896

3792

5688

7584

9480

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

616

1232

1848

2464

3080

<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:

0.446

Hom.:

2592

Bravo

AF:

0.455

Asia WGS

AF:

0.262

AC:

913

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.30

CADD

Benign

1.3

(source)

DANN

Benign

0.81

PhyloP100

-0.31

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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