dbSNP rs2820072: CHIA:c.314+267A>C (chr1-111314863-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_201653.4(CHIA):c.314+267A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.561 in 462,896 control chromosomes in the GnomAD database, including 74,303 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 0.56 ( 23923 hom., cov: 31)

Exomes 𝑓: 0.56 ( 50380 hom. )

Consequence

CHIA
NM_201653.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.501

Publications

6 publications found

Variant links:

Genes affected

CHIA (HGNC:17432): (chitinase acidic) The protein encoded by this gene degrades chitin, which is found in the cell wall of most fungi as well as in arthropods and some nematodes. The encoded protein can also stimulate interleukin 13 expression, and variations in this gene can lead to asthma susceptibility. Several transcript variants encoding a few different isoforms have been found for this gene. [provided by RefSeq, Apr 2012]

CHIA links:

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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=-0.81).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_201653.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CHIA	NM_201653.4	MANE Select	c.314+267A>C	intron	N/A	NP_970615.2	Q9BZP6-1
CHIA	NM_001258001.2		c.-11+267A>C	intron	N/A	NP_001244930.1	Q9BZP6-2
CHIA	NM_001258003.2		c.-11+267A>C	intron	N/A	NP_001244932.1	Q9BZP6-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CHIA	ENST00000369740.6	TSL:1 MANE Select	c.314+267A>C	intron	N/A	ENSP00000358755.1	Q9BZP6-1
CHIA	ENST00000422815.5	TSL:1	c.146+267A>C	intron	N/A	ENSP00000387671.1	Q5VUV5
CHIA	ENST00000430615.1	TSL:1	c.-11+267A>C	intron	N/A	ENSP00000391132.1	Q9BZP6-2

Frequencies

GnomAD3 genomes

AF:

0.557

AC:

84641

AN:

151960

Hom.:

23909

Cov.:

show subpopulations

Gnomad AFR

AF:

0.577

Gnomad AMI

AF:

0.524

Gnomad AMR

AF:

0.392

Gnomad ASJ

AF:

0.512

Gnomad EAS

AF:

0.453

Gnomad SAS

AF:

0.652

Gnomad FIN

AF:

0.569

Gnomad MID

AF:

0.608

Gnomad NFE

AF:

0.585

Gnomad OTH

AF:

0.519

GnomAD4 exome

AF:

0.563

AC:

175073

AN:

310818

Hom.:

50380

Cov.:

AF XY:

0.568

AC XY:

91978

AN XY:

161986

show subpopulations

African (AFR)

AF:

0.582

AC:

5010

AN:

8602

American (AMR)

AF:

0.333

AC:

3664

AN:

11006

Ashkenazi Jewish (ASJ)

AF:

0.518

AC:

5402

AN:

10436

East Asian (EAS)

AF:

0.445

AC:

9505

AN:

21362

South Asian (SAS)

AF:

0.656

AC:

17299

AN:

26364

European-Finnish (FIN)

AF:

0.564

AC:

11102

AN:

19688

Middle Eastern (MID)

AF:

0.599

AC:

930

AN:

1552

European-Non Finnish (NFE)

AF:

0.579

AC:

111757

AN:

192864

Other (OTH)

AF:

0.549

AC:

10404

AN:

18944

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

3494

6989

10483

13978

17472

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

476

952

1428

1904

2380

<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:

0.557

AC:

84706

AN:

152078

Hom.:

23923

Cov.:

AF XY:

0.556

AC XY:

41348

AN XY:

74328

show subpopulations

African (AFR)

AF:

0.578

AC:

23965

AN:

41482

American (AMR)

AF:

0.391

AC:

5976

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.512

AC:

1776

AN:

3468

East Asian (EAS)

AF:

0.453

AC:

2341

AN:

5168

South Asian (SAS)

AF:

0.651

AC:

3137

AN:

4820

European-Finnish (FIN)

AF:

0.569

AC:

6008

AN:

10552

Middle Eastern (MID)

AF:

0.629

AC:

185

AN:

294

European-Non Finnish (NFE)

AF:

0.585

AC:

39747

AN:

67990

Other (OTH)

AF:

0.518

AC:

1095

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1913

3826

5738

7651

9564

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

740

1480

2220

2960

3700

<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:

0.557

Hom.:

31525

Bravo

AF:

0.534

Asia WGS

AF:

0.522

AC:

1820

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

(source)

DANN

Benign

0.87

PhyloP100

0.50

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over