rs4240529

Positions:

• chr1-111282122-A-G

Variant summary

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

The NR_003928.2(CHIAP2):​n.602A>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 NR_003928.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.356

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
CHIAP2	NR_003928.2	n.602A>G		non_coding_transcript_exon_variant	2/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHIAP2	ENST00000369743.8	n.628A>G		non_coding_transcript_exon_variant	3/9	5
CHIAP2	ENST00000532686.5	n.258-297A>G		intron_variant, non_coding_transcript_variant
CHIAP2	ENST00000456752.6	n.336+261A>G		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR exome AF: 0.432

Gnomad4 AMR exome AF: 0.801

Gnomad4 ASJ exome AF: 0.651

Gnomad4 EAS exome AF: 0.923

Gnomad4 SAS exome AF: 0.691

Gnomad4 FIN exome AF: 0.675

Gnomad4 NFE exome AF: 0.659

Gnomad4 OTH exome AF: 0.668

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

Gnomad4 AFR AF: 0.573

Gnomad4 AMR AF: 0.803

Gnomad4 ASJ AF: 0.717

Gnomad4 EAS AF: 0.943

Gnomad4 SAS AF: 0.784

Gnomad4 FIN AF: 0.748

Gnomad4 NFE AF: 0.718

Gnomad4 OTH AF: 0.710

Alfa AF: 0.717 Hom.: 21069

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4240529; hg19: chr1-111824744;