rs2256721

chr1-111320330-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_201653.4(CHIA):c.1295T>G(p.Val432Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.69 in 1,613,944 control chromosomes in the GnomAD database, including 389,913 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

• Frequency:
  • Genomes: 𝑓 0.69 (37018 hom., cov: 32)
  • Exomes 𝑓: 0.69 (352895 hom.)
• Consequence: CHIA NM_201653.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.29

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=9.624317E-7).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.768 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHIA	NM_201653.4	c.1295T>G	p.Val432Gly	missense_variant	12/12	ENST00000369740.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHIA	ENST00000369740.6	c.1295T>G	p.Val432Gly	missense_variant	12/12	1	NM_201653.4	P1
	ENST00000426321.1	n.149-2403A>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.691 AC: 105031 AN: 152014 Hom.: 36992 Cov.: 32

Gnomad AFR AF: 0.774

Gnomad AMI AF: 0.771

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.457

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.643

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.652

GnomAD3 exomes AF: 0.639 AC: 160500 AN: 251014 Hom.: 53895 AF XY: 0.655 AC XY: 88914 AN XY: 135688

Gnomad AFR exome AF: 0.772

Gnomad AMR exome AF: 0.349

Gnomad ASJ exome AF: 0.706

Gnomad EAS exome AF: 0.454

Gnomad SAS exome AF: 0.758

Gnomad FIN exome AF: 0.637

Gnomad NFE exome AF: 0.700

Gnomad OTH exome AF: 0.658

GnomAD4 exome AF: 0.690 AC: 1009264 AN: 1461812 Hom.: 352895 Cov.: 71 AF XY: 0.694 AC XY: 504802 AN XY: 727204

Gnomad4 AFR exome AF: 0.781

Gnomad4 AMR exome AF: 0.366

Gnomad4 ASJ exome AF: 0.704

Gnomad4 EAS exome AF: 0.458

Gnomad4 SAS exome AF: 0.756

Gnomad4 FIN exome AF: 0.639

Gnomad4 NFE exome AF: 0.706

Gnomad4 OTH exome AF: 0.685

GnomAD4 genome AF: 0.691 AC: 105106 AN: 152132 Hom.: 37018 Cov.: 32 AF XY: 0.686 AC XY: 50995 AN XY: 74362

Gnomad4 AFR AF: 0.775

Gnomad4 AMR AF: 0.493

Gnomad4 ASJ AF: 0.699

Gnomad4 EAS AF: 0.457

Gnomad4 SAS AF: 0.742

Gnomad4 FIN AF: 0.643

Gnomad4 NFE AF: 0.705

Gnomad4 OTH AF: 0.650

Alfa AF: 0.698 Hom.: 90816

Bravo AF: 0.673

TwinsUK AF: 0.702 AC: 2602

ALSPAC AF: 0.718 AC: 2769

ESP6500AA AF: 0.768 AC: 3382

ESP6500EA AF: 0.697 AC: 5991

ExAC AF: 0.655 AC: 79499

Asia WGS AF: 0.573 AC: 1996 AN: 3478

EpiCase AF: 0.715

EpiControl AF: 0.708

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.041
BayesDel_addAF	Benign	-0.59	T
BayesDel_noAF	Benign	-0.47
Cadd	Benign	9.4
Dann	Benign	0.80
Eigen	Benign	-1.3
Eigen_PC	Benign	-1.0
FATHMM_MKL	Benign	0.014	N
LIST_S2	Benign	0.011	T;.;.;T;T;.;T;T
MetaRNN	Benign	9.6e-7	T;T;T;T;T;T;T;T
MetaSVM	Benign	-0.96	T
MutationTaster	Benign	0.52	P;P;P;P;P;P
PrimateAI	Benign	0.32	T
PROVEAN	Benign	4.7	N;N;N;N;N;N;N;N
REVEL	Benign	0.29
Sift	Benign	1.0	T;T;T;T;T;T;T;T
Sift4G	Benign	1.0	T;T;T;T;T;T;T;T
Polyphen		0.0	.;.;B;.;B;.;.;.
Vest4		0.058, 0.041, 0.055, 0.036, 0.070, 0.039
MPC		0.030
ClinPred		0.0016	T
GERP RS		1.5
Varity_R		0.050
gMVP		0.66

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

Other links and lift over

dbSNP: rs2256721; hg19: chr1-111862952; COSMIC: COSV58473784; COSMIC: COSV58473784;