Variant chr1-111285127-G-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000532686.5(CHIAP2):n.1176+5G>T variant causes a splice donor 5th base, intron, non coding transcript change. The variant allele was found at a frequency of 0.253 in 158,878 control chromosomes in the GnomAD database, including 5,445 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 0.25 ( 5189 hom., cov: 32)

Exomes 𝑓: 0.24 ( 256 hom. )

Consequence

CHIAP2
ENST00000532686.5 splice_donor_5th_base, intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.11

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=-0.54).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.393 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.1822G>T		non_coding_transcript_exon_variant	8/8

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
CHIAP2	ENST00000369743.8 linkuse as main transcript	n.1848G>T	non_coding_transcript_exon_variant	9/9	5
CHIAP2	ENST00000532686.5 linkuse as main transcript	n.1176+5G>T	splice_donor_5th_base_variant, intron_variant, non_coding_transcript_variant
CHIAP2	ENST00000449687.1 linkuse as main transcript	n.323+5G>T	splice_donor_5th_base_variant, intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.254

AC:

38614

AN:

151936

Hom.:

5184

Cov.:

show subpopulations

Gnomad AFR

AF:

0.201

Gnomad AMI

AF:

0.282

Gnomad AMR

AF:

0.354

Gnomad ASJ

AF:

0.260

Gnomad EAS

AF:

0.408

Gnomad SAS

AF:

0.274

Gnomad FIN

AF:

0.235

Gnomad MID

AF:

0.274

Gnomad NFE

AF:

0.253

Gnomad OTH

AF:

0.262

GnomAD4 exome

AF:

0.241

AC:

1647

AN:

6824

Hom.:

256

Cov.:

AF XY:

0.240

AC XY:

919

AN XY:

3822

show subpopulations

Gnomad4 AFR exome

AF:

0.143

Gnomad4 AMR exome

AF:

0.422

Gnomad4 ASJ exome

AF:

0.208

Gnomad4 EAS exome

AF:

0.455

Gnomad4 SAS exome

AF:

0.257

Gnomad4 FIN exome

AF:

0.216

Gnomad4 NFE exome

AF:

0.234

Gnomad4 OTH exome

AF:

0.223

GnomAD4 genome

AF:

0.254

AC:

38628

AN:

152054

Hom.:

5189

Cov.:

AF XY:

0.257

AC XY:

19085

AN XY:

74308

show subpopulations

Gnomad4 AFR

AF:

0.201

Gnomad4 AMR

AF:

0.355

Gnomad4 ASJ

AF:

0.260

Gnomad4 EAS

AF:

0.407

Gnomad4 SAS

AF:

0.275

Gnomad4 FIN

AF:

0.235

Gnomad4 NFE

AF:

0.253

Gnomad4 OTH

AF:

0.260

Alfa

AF:

0.262

Hom.:

7418

Bravo

AF:

0.265

Asia WGS

AF:

0.331

AC:

1151

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

CADD

Benign

DANN

Benign

0.82

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