rs4272622

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000369743.8(CHIAP2):​n.1147+77T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000133 in 753,662 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000013 (0 hom.)
• Consequence: CHIAP2 ENST00000369743.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178
• Publications: 0 publications found

Genes affected

CHIAP2 (HGNC:):

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

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHIAP2	NR_003928.2	n.1121+77T>A		intron_variant	Intron 3 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHIAP2	ENST00000369743.8	n.1147+77T>A		intron_variant	Intron 4 of 8	5
CHIAP2	ENST00000456752.6	n.559+77T>A		intron_variant	Intron 4 of 6	5
CHIAP2	ENST00000532686.5	n.480+77T>A		intron_variant	Intron 5 of 10	6

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000133 AC: 1 AN: 753662 Hom.: 0 Cov.: 10 AF XY: 0.00000259 AC XY: 1 AN XY: 385692

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 18206

American (AMR) AF: 0.00 AC: 0 AN: 23538

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 16862

East Asian (EAS) AF: 0.00 AC: 0 AN: 32974

South Asian (SAS) AF: 0.0000181 AC: 1 AN: 55256

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 45160

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2606

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 523074

Other (OTH) AF: 0.00 AC: 0 AN: 35986

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	8.1
DANN	Benign	0.79
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;