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GeneBe

1-111318579-C-A

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_201653.4(CHIA):c.816C>A(p.Ile272=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00535 in 1,614,194 control chromosomes in the GnomAD database, including 36 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0039 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0055 ( 36 hom. )

Consequence

CHIA
NM_201653.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.121
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.35).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 1-111318579-C-A is Benign according to our data. Variant chr1-111318579-C-A is described in ClinVar as [Benign]. Clinvar id is 782080.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=0.121 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAdExome at 10 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CHIANM_201653.4 linkuse as main transcriptc.816C>A p.Ile272= synonymous_variant 9/12 ENST00000369740.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CHIAENST00000369740.6 linkuse as main transcriptc.816C>A p.Ile272= synonymous_variant 9/121 NM_201653.4 P1Q9BZP6-1
ENST00000426321.1 linkuse as main transcriptn.149-652G>T intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00388
AC:
590
AN:
152206
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000796
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00281
Gnomad ASJ
AF:
0.00259
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.000621
Gnomad FIN
AF:
0.0109
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00551
Gnomad OTH
AF:
0.00478
GnomAD3 exomes
AF:
0.00461
AC:
1159
AN:
251396
Hom.:
10
AF XY:
0.00456
AC XY:
619
AN XY:
135856
show subpopulations
Gnomad AFR exome
AF:
0.000738
Gnomad AMR exome
AF:
0.00237
Gnomad ASJ exome
AF:
0.00258
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00137
Gnomad FIN exome
AF:
0.0116
Gnomad NFE exome
AF:
0.00625
Gnomad OTH exome
AF:
0.00587
GnomAD4 exome
AF:
0.00551
AC:
8051
AN:
1461870
Hom.:
36
Cov.:
32
AF XY:
0.00531
AC XY:
3860
AN XY:
727234
show subpopulations
Gnomad4 AFR exome
AF:
0.000747
Gnomad4 AMR exome
AF:
0.00233
Gnomad4 ASJ exome
AF:
0.00187
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.00139
Gnomad4 FIN exome
AF:
0.0120
Gnomad4 NFE exome
AF:
0.00611
Gnomad4 OTH exome
AF:
0.00510
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00387
AC:
590
AN:
152324
Hom.:
0
Cov.:
32
AF XY:
0.00416
AC XY:
310
AN XY:
74472
show subpopulations
Gnomad4 AFR
AF:
0.000794
Gnomad4 AMR
AF:
0.00281
Gnomad4 ASJ
AF:
0.00259
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.000622
Gnomad4 FIN
AF:
0.0109
Gnomad4 NFE
AF:
0.00551
Gnomad4 OTH
AF:
0.00473
Alfa
AF:
0.00485
Hom.:
1
Bravo
AF:
0.00322
EpiCase
AF:
0.00529
EpiControl
AF:
0.00528

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeJan 08, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.35
Cadd
Benign
0.77
Dann
Benign
0.65

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs139093708; hg19: chr1-111861201; API