1-167157013-C-T

Position:

• chr1-167157013-C-T

Variant summary

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

The ENST00000632571.1(GPA33):​c.-282+9270G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.528 in 151,870 control chromosomes in the GnomAD database, including 21,525 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 0.53 (21525 hom., cov: 31)
• Consequence: GPA33 ENST00000632571.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.112

Genes affected

GPA33 (HGNC:4445): (glycoprotein A33) The glycoprotein encoded by this gene is a cell surface antigen that is expressed in greater than 95% of human colon cancers. The open reading frame encodes a 319-amino acid polypeptide having a putative secretory signal sequence and 3 potential glycosylation sites. The predicted mature protein has a 213-amino acid extracellular region, a single transmembrane domain, and a 62-amino acid intracellular tail. The sequence of the extracellular region contains 2 domains characteristic of the CD2 subgroup of the immunoglobulin (Ig) superfamily. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GPA33	ENST00000632571.1	c.-282+9270G>A		intron_variant		4		ENSP00000488407.1

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80184 AN: 151752 Hom.: 21492 Cov.: 31

Gnomad AFR AF: 0.522

Gnomad AMI AF: 0.625

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.560

Gnomad EAS AF: 0.685

Gnomad SAS AF: 0.649

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.528 AC: 80256 AN: 151870 Hom.: 21525 Cov.: 31 AF XY: 0.531 AC XY: 39379 AN XY: 74212

Gnomad4 AFR AF: 0.522

Gnomad4 AMR AF: 0.581

Gnomad4 ASJ AF: 0.560

Gnomad4 EAS AF: 0.685

Gnomad4 SAS AF: 0.650

Gnomad4 FIN AF: 0.484

Gnomad4 NFE AF: 0.504

Gnomad4 OTH AF: 0.548

Alfa AF: 0.515 Hom.: 32265

Bravo AF: 0.537

Asia WGS AF: 0.661 AC: 2297 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.3
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs869714; hg19: chr1-167126250;