chr1-111319154-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_201653.4(CHIA):c.950G>A(p.Gly317Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00134 in 1,612,148 control chromosomes in the GnomAD database, including 24 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0064 ( 8 hom., cov: 33)
Exomes 𝑓: 0.00082 ( 16 hom. )
Consequence
CHIA
NM_201653.4 missense
NM_201653.4 missense
Scores
16
Clinical Significance
Conservation
PhyloP100: -3.05
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.006751001).
BP6
?
Variant 1-111319154-G-A is Benign according to our data. Variant chr1-111319154-G-A is described in ClinVar as [Benign]. Clinvar id is 711970.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00645 (969/150298) while in subpopulation AFR AF= 0.0228 (907/39716). AF 95% confidence interval is 0.0216. There are 8 homozygotes in gnomad4. There are 487 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 8 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHIA | NM_201653.4 | c.950G>A | p.Gly317Glu | missense_variant | 10/12 | ENST00000369740.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHIA | ENST00000369740.6 | c.950G>A | p.Gly317Glu | missense_variant | 10/12 | 1 | NM_201653.4 | P1 | |
ENST00000426321.1 | n.149-1227C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00644 AC: 967AN: 150198Hom.: 8 Cov.: 33
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00160 AC: 399AN: 249240Hom.: 4 AF XY: 0.00124 AC XY: 167AN XY: 134972
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GnomAD4 exome AF: 0.000819 AC: 1197AN: 1461850Hom.: 16 Cov.: 62 AF XY: 0.000752 AC XY: 547AN XY: 727238
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GnomAD4 genome ? AF: 0.00645 AC: 969AN: 150298Hom.: 8 Cov.: 33 AF XY: 0.00662 AC XY: 487AN XY: 73532
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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 submitter | clinical testing | Invitae | Aug 21, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;.;.;T;T;.;T;T
MetaRNN
Benign
T;T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
N;N;N;N;N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;N;N;N;N;N;N;N
REVEL
Benign
Sift
Benign
T;T;T;T;T;T;T;T
Sift4G
Benign
T;T;T;T;T;T;T;T
Polyphen
0.0
.;.;B;.;B;.;.;.
Vest4
0.070, 0.090, 0.091, 0.076
MVP
MPC
0.030
ClinPred
T
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at