Variant 1-111282813-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_003928.2(CHIAP2):n.1121+77T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 904,806 control chromosomes in the GnomAD database, including 17,699 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 0.17 ( 2755 hom., cov: 32)

Exomes 𝑓: 0.19 ( 14944 hom. )

Consequence

CHIAP2
NR_003928.2 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.178

Variant links:

Genes affected

CHIAP2 (HGNC:44463): (chitinase, acidic pseudogene 2)

CHIAP2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHIAP2	NR_003928.2 linkuse as main transcript	n.1121+77T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
CHIAP2	ENST00000369743.8 linkuse as main transcript	n.1147+77T>C	intron_variant, non_coding_transcript_variant	5
CHIAP2	ENST00000532686.5 linkuse as main transcript	n.480+77T>C	intron_variant, non_coding_transcript_variant
CHIAP2	ENST00000456752.6 linkuse as main transcript	n.559+77T>C	intron_variant, non_coding_transcript_variant	5

Frequencies

GnomAD3 genomes

AF:

0.170

AC:

25836

AN:

152048

Hom.:

2748

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0656

Gnomad AMI

AF:

0.254

Gnomad AMR

AF:

0.306

Gnomad ASJ

AF:

0.156

Gnomad EAS

AF:

0.360

Gnomad SAS

AF:

0.226

Gnomad FIN

AF:

0.188

Gnomad MID

AF:

0.165

Gnomad NFE

AF:

0.181

Gnomad OTH

AF:

0.183

GnomAD4 exome

AF:

0.189

AC:

142204

AN:

752640

Hom.:

14944

Cov.:

AF XY:

0.190

AC XY:

73061

AN XY:

385198

show subpopulations

Gnomad4 AFR exome

AF:

0.0579

Gnomad4 AMR exome

AF:

0.378

Gnomad4 ASJ exome

AF:

0.156

Gnomad4 EAS exome

AF:

0.337

Gnomad4 SAS exome

AF:

0.223

Gnomad4 FIN exome

AF:

0.175

Gnomad4 NFE exome

AF:

0.174

Gnomad4 OTH exome

AF:

0.187

GnomAD4 genome

AF:

0.170

AC:

25848

AN:

152166

Hom.:

2755

Cov.:

AF XY:

0.175

AC XY:

13010

AN XY:

74384

show subpopulations

Gnomad4 AFR

AF:

0.0654

Gnomad4 AMR

AF:

0.307

Gnomad4 ASJ

AF:

0.156

Gnomad4 EAS

AF:

0.360

Gnomad4 SAS

AF:

0.227

Gnomad4 FIN

AF:

0.188

Gnomad4 NFE

AF:

0.181

Gnomad4 OTH

AF:

0.181

Alfa

AF:

0.180

Hom.:

1474

Bravo

AF:

0.179

Asia WGS

AF:

0.265

AC:

919

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

8.3

DANN

Benign

0.81

Splicing

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over