Genetic Variant CHIAP2:n.1848G>T (chr1-111285127-G-T) – 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.1848G>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.253 in 158,878 control chromosomes in the GnomAD database, including 5,445 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 0.25 ( 5189 hom., cov: 32)

Exomes 𝑓: 0.24 ( 256 hom. )

Consequence

CHIAP2
ENST00000369743.8 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.11

Publications

14 publications found

Variant links:

COSMIC-nc: COSV63872586

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=-0.54).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHIAP2	NR_003928.2 link	n.1822G>T		non_coding_transcript_exon_variant	Exon 8 of 8

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
CHIAP2	ENST00000369743.8 link	n.1848G>T	non_coding_transcript_exon_variant	Exon 9 of 9	5
CHIAP2	ENST00000449687.1 link	n.323+5G>T	splice_region_variant, intron_variant	Intron 3 of 3	3
CHIAP2	ENST00000532686.5 link	n.1176+5G>T	splice_region_variant, intron_variant	Intron 10 of 10	6

Frequencies

GnomAD3 genomes

AF:

0.254

AC:

38614

AN:

151936

Hom.:

5184

Cov.:

show subpopulations

Gnomad AFR

AF:

0.201

Gnomad AMI

AF:

0.282

Gnomad AMR

AF:

0.354

Gnomad ASJ

AF:

0.260

Gnomad EAS

AF:

0.408

Gnomad SAS

AF:

0.274

Gnomad FIN

AF:

0.235

Gnomad MID

AF:

0.274

Gnomad NFE

AF:

0.253

Gnomad OTH

AF:

0.262

GnomAD4 exome

AF:

0.241

AC:

1647

AN:

6824

Hom.:

256

Cov.:

AF XY:

0.240

AC XY:

919

AN XY:

3822

show subpopulations

African (AFR)

AF:

0.143

AC:

AN:

American (AMR)

AF:

0.422

AC:

AN:

230

Ashkenazi Jewish (ASJ)

AF:

0.208

AC:

AN:

106

East Asian (EAS)

AF:

0.455

AC:

AN:

132

South Asian (SAS)

AF:

0.257

AC:

292

AN:

1136

European-Finnish (FIN)

AF:

0.216

AC:

368

AN:

1700

Middle Eastern (MID)

AF:

0.0714

AC:

AN:

European-Non Finnish (NFE)

AF:

0.234

AC:

726

AN:

3108

Other (OTH)

AF:

0.223

AC:

AN:

328

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

106

158

211

264

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.254

AC:

38628

AN:

152054

Hom.:

5189

Cov.:

AF XY:

0.257

AC XY:

19085

AN XY:

74308

show subpopulations

African (AFR)

AF:

0.201

AC:

8320

AN:

41480

American (AMR)

AF:

0.355

AC:

5417

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.260

AC:

904

AN:

3472

East Asian (EAS)

AF:

0.407

AC:

2096

AN:

5144

South Asian (SAS)

AF:

0.275

AC:

1325

AN:

4820

European-Finnish (FIN)

AF:

0.235

AC:

2481

AN:

10548

Middle Eastern (MID)

AF:

0.284

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.253

AC:

17195

AN:

67990

Other (OTH)

AF:

0.260

AC:

550

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1439

2879

4318

5758

7197

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

412

824

1236

1648

2060

<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:

0.262

Hom.:

9408

Bravo

AF:

0.265

Asia WGS

AF:

0.331

AC:

1151

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

CADD

Benign

(source)

DANN

Benign

0.82

PhyloP100

5.1

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