Genetic Variant CHIAP2:n.1147+77T>C (chr1-111282813-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000369743.8(CHIAP2):n.1147+77T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 904,806 control chromosomes in the GnomAD database, including 17,699 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 0.17 ( 2755 hom., cov: 32)

Exomes 𝑓: 0.19 ( 14944 hom. )

Consequence

CHIAP2
ENST00000369743.8 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.178

Publications

6 publications found

Variant links:

COSMIC-nc: COSV63873191

Genes affected

CHIAP2 (HGNC:):

CHIAP2 links:

CHIAP2 (HGNC:44463): (chitinase, acidic pseudogene 2)

CHIAP2 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=-0.86).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHIAP2	NR_003928.2 link	n.1121+77T>C		intron_variant	Intron 3 of 7

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
CHIAP2	ENST00000369743.8 link	n.1147+77T>C	intron_variant	Intron 4 of 8	5
CHIAP2	ENST00000456752.6 link	n.559+77T>C	intron_variant	Intron 4 of 6	5
CHIAP2	ENST00000532686.5 link	n.480+77T>C	intron_variant	Intron 5 of 10	6

Frequencies

GnomAD3 genomes

AF:

0.170

AC:

25836

AN:

152048

Hom.:

2748

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0656

Gnomad AMI

AF:

0.254

Gnomad AMR

AF:

0.306

Gnomad ASJ

AF:

0.156

Gnomad EAS

AF:

0.360

Gnomad SAS

AF:

0.226

Gnomad FIN

AF:

0.188

Gnomad MID

AF:

0.165

Gnomad NFE

AF:

0.181

Gnomad OTH

AF:

0.183

GnomAD4 exome

AF:

0.189

AC:

142204

AN:

752640

Hom.:

14944

Cov.:

AF XY:

0.190

AC XY:

73061

AN XY:

385198

show subpopulations

African (AFR)

AF:

0.0579

AC:

1054

AN:

18198

American (AMR)

AF:

0.378

AC:

8877

AN:

23496

Ashkenazi Jewish (ASJ)

AF:

0.156

AC:

2624

AN:

16846

East Asian (EAS)

AF:

0.337

AC:

11098

AN:

32946

South Asian (SAS)

AF:

0.223

AC:

12316

AN:

55190

European-Finnish (FIN)

AF:

0.175

AC:

7889

AN:

45114

Middle Eastern (MID)

AF:

0.179

AC:

466

AN:

2604

European-Non Finnish (NFE)

AF:

0.174

AC:

91141

AN:

522304

Other (OTH)

AF:

0.187

AC:

6739

AN:

35942

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

5535

11070

16604

22139

27674

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2302

4604

6906

9208

11510

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.170

AC:

25848

AN:

152166

Hom.:

2755

Cov.:

AF XY:

0.175

AC XY:

13010

AN XY:

74384

show subpopulations

African (AFR)

AF:

0.0654

AC:

2714

AN:

41524

American (AMR)

AF:

0.307

AC:

4689

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.156

AC:

543

AN:

3470

East Asian (EAS)

AF:

0.360

AC:

1861

AN:

5172

South Asian (SAS)

AF:

0.227

AC:

1095

AN:

4820

European-Finnish (FIN)

AF:

0.188

AC:

1986

AN:

10580

Middle Eastern (MID)

AF:

0.170

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.181

AC:

12295

AN:

68004

Other (OTH)

AF:

0.181

AC:

383

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1067

2134

3200

4267

5334

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

290

580

870

1160

1450

<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:

0.179

Hom.:

2024

Bravo

AF:

0.179

Asia WGS

AF:

0.265

AC:

919

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

8.3

(source)

DANN

Benign

0.81

PhyloP100

0.18

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over