ENST00000423668.1:n.305+651G>T

Variant names:

• chr1-111366091-C-A
• rs1361049
• ENST00000423668.1:n.305+651G>T

Variant summary

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

The ENST00000423668.1(CHIAP3):​n.305+651G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.496 in 151,950 control chromosomes in the GnomAD database, including 19,975 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 0.50 (19975 hom., cov: 32)
• Consequence: CHIAP3 ENST00000423668.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.983
• Publications: 3 publications found

Genes affected

CHIAP3 (HGNC:44464): (chitinase, acidic pseudogene 3)

ENSG00000296639 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.738 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378904	XR_001737802.1	n.1090-2459G>T		intron_variant	Intron 1 of 2
LOC105378904	XR_947704.2	n.1119+2373G>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHIAP3	ENST00000423668.1	n.305+651G>T		intron_variant	Intron 2 of 8	6
ENSG00000296639	ENST00000740945.1	n.471+2373G>T		intron_variant	Intron 2 of 3
ENSG00000296639	ENST00000740946.1	n.76-2459G>T		intron_variant	Intron 1 of 2
ENSG00000296639	ENST00000740947.1	n.66-2459G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.496 AC: 75262 AN: 151832 Hom.: 19956 Cov.: 32

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.759

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.531

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.496 AC: 75330 AN: 151950 Hom.: 19975 Cov.: 32 AF XY: 0.501 AC XY: 37208 AN XY: 74252

African (AFR) AF: 0.303 AC: 12553 AN: 41436

American (AMR) AF: 0.653 AC: 9977 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1612 AN: 3460

East Asian (EAS) AF: 0.758 AC: 3913 AN: 5164

South Asian (SAS) AF: 0.521 AC: 2512 AN: 4818

European-Finnish (FIN) AF: 0.582 AC: 6134 AN: 10544

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.544 AC: 36948 AN: 67942

Other (OTH) AF: 0.534 AC: 1123 AN: 2104

Alfa AF: 0.531 Hom.: 39819

Bravo AF: 0.499

Asia WGS AF: 0.612 AC: 2124 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	5.8
DANN	Benign	0.49
PhyloP100		0.98

Splicing

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

Other links and lift over

dbSNP: rs1361049; hg19: chr1-111908713;