rs1361049

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr1-111366091-C-A
• chr1-111366091-C-G

Variant summary

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

The ENST00000740945.1(ENSG00000296639):​n.471+2373G>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: ENSG00000296639 ENST00000740945.1 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000740945.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHIAP3	ENST00000423668.1	TSL:6	n.305+651G>T		intron	N/A
	ENSG00000296639	ENST00000740945.1		n.471+2373G>T		intron	N/A
	ENSG00000296639	ENST00000740946.1		n.76-2459G>T		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1361049;

hg19: chr1-111908713;