chr1-111282813-T-C

Variant names:

• chr1-111282813-T-C
• rs4272622
• ENST00000369743.8:n.1147+77T>C

Variant summary

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

The ENST00000369743.8(CHIAP2):​n.1147+77T>C variant causes a intron 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 ENST00000369743.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178
• Publications: 6 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000369743.8. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHIAP2	NR_003928.2		n.1121+77T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHIAP2	ENST00000369743.8	TSL:5	n.1147+77T>C		intron	N/A
	CHIAP2	ENST00000456752.6	TSL:5	n.559+77T>C		intron	N/A
	CHIAP2	ENST00000532686.5	TSL:6	n.480+77T>C		intron	N/A

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

African (AFR) AF: 0.0579 AC: 1054 AN: 18198

American (AMR) AF: 0.378 AC: 8877 AN: 23496

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 2624 AN: 16846

East Asian (EAS) AF: 0.337 AC: 11098 AN: 32946

South Asian (SAS) AF: 0.223 AC: 12316 AN: 55190

European-Finnish (FIN) AF: 0.175 AC: 7889 AN: 45114

Middle Eastern (MID) AF: 0.179 AC: 466 AN: 2604

European-Non Finnish (NFE) AF: 0.174 AC: 91141 AN: 522304

Other (OTH) AF: 0.187 AC: 6739 AN: 35942

GnomAD4 genome AF: 0.170 AC: 25848 AN: 152166 Hom.: 2755 Cov.: 32 AF XY: 0.175 AC XY: 13010 AN XY: 74384

African (AFR) AF: 0.0654 AC: 2714 AN: 41524

American (AMR) AF: 0.307 AC: 4689 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 543 AN: 3470

East Asian (EAS) AF: 0.360 AC: 1861 AN: 5172

South Asian (SAS) AF: 0.227 AC: 1095 AN: 4820

European-Finnish (FIN) AF: 0.188 AC: 1986 AN: 10580

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.181 AC: 12295 AN: 68004

Other (OTH) AF: 0.181 AC: 383 AN: 2116

Alfa AF: 0.179 Hom.: 2024

Bravo AF: 0.179

Asia WGS AF: 0.265 AC: 919 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.3
DANN	Benign	0.81
PhyloP100		0.18

Splicing

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

Other links and lift over

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