rs1361049

chr1-111366091-C-Achr1-111366091-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000423668.1(CHIAP3):n.305+651G>T variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.983

Genes affected

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

LOC105378904 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105378904	XR_947704.2	n.1119+2373G>T		intron_variant, non_coding_transcript_variant
LOC105378904	XR_001737802.1	n.1090-2459G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHIAP3	ENST00000423668.1	n.305+651G>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.303

Gnomad4 AMR AF: 0.653

Gnomad4 ASJ AF: 0.466

Gnomad4 EAS AF: 0.758

Gnomad4 SAS AF: 0.521

Gnomad4 FIN AF: 0.582

Gnomad4 NFE AF: 0.544

Gnomad4 OTH AF: 0.534

Alfa AF: 0.534 Hom.: 29414

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1361049; hg19: chr1-111908713;