1-111285127-G-T

Variant names:

• chr1-111285127-G-T
• rs11102233
• ENST00000369743.8:n.1848G>T

Variant summary

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

The ENST00000449687.1(CHIAP2):​n.323+5G>T variant causes a splice region, intron 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 ENST00000449687.1 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.11
• Publications: 14 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=-0.54).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000449687.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHIAP2	NR_003928.2		n.1822G>T		non_coding_transcript_exon	Exon 8 of 8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHIAP2	ENST00000369743.8	TSL:5	n.1848G>T		non_coding_transcript_exon	Exon 9 of 9
	CHIAP2	ENST00000449687.1	TSL:3	n.323+5G>T		splice_region intron	N/A
	CHIAP2	ENST00000532686.5	TSL:6	n.1176+5G>T		splice_region intron	N/A

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38614 AN: 151936 Hom.: 5184 Cov.: 32

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.: 0 AF XY: 0.240 AC XY: 919 AN XY: 3822

African (AFR) AF: 0.143 AC: 6 AN: 42

American (AMR) AF: 0.422 AC: 97 AN: 230

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 22 AN: 106

East Asian (EAS) AF: 0.455 AC: 60 AN: 132

South Asian (SAS) AF: 0.257 AC: 292 AN: 1136

European-Finnish (FIN) AF: 0.216 AC: 368 AN: 1700

Middle Eastern (MID) AF: 0.0714 AC: 3 AN: 42

European-Non Finnish (NFE) AF: 0.234 AC: 726 AN: 3108

Other (OTH) AF: 0.223 AC: 73 AN: 328

GnomAD4 genome AF: 0.254 AC: 38628 AN: 152054 Hom.: 5189 Cov.: 32 AF XY: 0.257 AC XY: 19085 AN XY: 74308

African (AFR) AF: 0.201 AC: 8320 AN: 41480

American (AMR) AF: 0.355 AC: 5417 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.260 AC: 904 AN: 3472

East Asian (EAS) AF: 0.407 AC: 2096 AN: 5144

South Asian (SAS) AF: 0.275 AC: 1325 AN: 4820

European-Finnish (FIN) AF: 0.235 AC: 2481 AN: 10548

Middle Eastern (MID) AF: 0.284 AC: 83 AN: 292

European-Non Finnish (NFE) AF: 0.253 AC: 17195 AN: 67990

Other (OTH) AF: 0.260 AC: 550 AN: 2116

Alfa AF: 0.262 Hom.: 9408

Bravo AF: 0.265

Asia WGS AF: 0.331 AC: 1151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	18
DANN	Benign	0.82
PhyloP100		5.1

Splicing

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

Other links and lift over

dbSNP: rs11102233; hg19: chr1-111827749; COSMIC: COSV63872586;