rs4240529

Variant names:

• chr1-111282122-A-G
• rs4240529
• ENST00000369743.8:n.628A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000369743.8(CHIAP2):​n.628A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.696 in 170,856 control chromosomes in the GnomAD database, including 42,184 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 0.70 (37652 hom., cov: 30)
  • Exomes 𝑓: 0.68 (4532 hom.)
• Consequence: CHIAP2 ENST00000369743.8 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.356
• Publications: 8 publications found

Genes affected

CHIAP2 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.921 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHIAP2	NR_003928.2	n.602A>G		non_coding_transcript_exon_variant	Exon 2 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHIAP2	ENST00000369743.8	n.628A>G		non_coding_transcript_exon_variant	Exon 3 of 9	5
CHIAP2	ENST00000456752.6	n.336+261A>G		intron_variant	Intron 2 of 6	5
CHIAP2	ENST00000532686.5	n.258-297A>G		intron_variant	Intron 3 of 10	6

Frequencies

GnomAD3 genomes AF: 0.698 AC: 106025 AN: 151792 Hom.: 37641 Cov.: 30

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.802

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.943

Gnomad SAS AF: 0.783

Gnomad FIN AF: 0.748

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.718

Gnomad OTH AF: 0.710

GnomAD4 exome AF: 0.680 AC: 12891 AN: 18946 Hom.: 4532 Cov.: 0 AF XY: 0.689 AC XY: 6695 AN XY: 9722

African (AFR) AF: 0.432 AC: 208 AN: 482

American (AMR) AF: 0.801 AC: 1490 AN: 1860

Ashkenazi Jewish (ASJ) AF: 0.651 AC: 289 AN: 444

East Asian (EAS) AF: 0.923 AC: 705 AN: 764

South Asian (SAS) AF: 0.691 AC: 949 AN: 1374

European-Finnish (FIN) AF: 0.675 AC: 456 AN: 676

Middle Eastern (MID) AF: 0.549 AC: 45 AN: 82

European-Non Finnish (NFE) AF: 0.659 AC: 8003 AN: 12148

Other (OTH) AF: 0.668 AC: 746 AN: 1116

GnomAD4 genome AF: 0.698 AC: 106079 AN: 151910 Hom.: 37652 Cov.: 30 AF XY: 0.705 AC XY: 52332 AN XY: 74242

African (AFR) AF: 0.573 AC: 23709 AN: 41376

American (AMR) AF: 0.803 AC: 12270 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.717 AC: 2487 AN: 3468

East Asian (EAS) AF: 0.943 AC: 4871 AN: 5166

South Asian (SAS) AF: 0.784 AC: 3771 AN: 4812

European-Finnish (FIN) AF: 0.748 AC: 7899 AN: 10556

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.718 AC: 48765 AN: 67932

Other (OTH) AF: 0.710 AC: 1498 AN: 2110

Alfa AF: 0.717 Hom.: 23226

Bravo AF: 0.700

Asia WGS AF: 0.813 AC: 2826 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.5
DANN	Benign	0.45
PhyloP100		-0.36

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4240529; hg19: chr1-111824744;