rs4272622

Positions:

• chr1-111282813-T-C
• chr1-111282813-T-G

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178

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=-0.86).
• 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	n.1121+77T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHIAP2	ENST00000369743.8	n.1147+77T>C		intron_variant, non_coding_transcript_variant		5
CHIAP2	ENST00000532686.5	n.480+77T>C		intron_variant, non_coding_transcript_variant
CHIAP2	ENST00000456752.6	n.559+77T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25836 AN: 152048 Hom.: 2748 Cov.: 32

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.: 10 AF XY: 0.190 AC XY: 73061 AN XY: 385198

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.: 32 AF XY: 0.175 AC XY: 13010 AN XY: 74384

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

Other links and lift over

dbSNP: rs4272622; hg19: chr1-111825435; COSMIC: COSV63873191;