ENST00000632571.1:c.-282+9270G>A

Variant names:

• chr1-167157013-C-T
• rs869714
• ENST00000632571.1:c.-282+9270G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000632571.1. 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
	GPA33	ENST00000632571.1	TSL:4	c.-282+9270G>A		intron	N/A	ENSP00000488407.1	A0A0J9YXH7

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

African (AFR) AF: 0.522 AC: 21638 AN: 41422

American (AMR) AF: 0.581 AC: 8864 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.560 AC: 1942 AN: 3470

East Asian (EAS) AF: 0.685 AC: 3519 AN: 5140

South Asian (SAS) AF: 0.650 AC: 3126 AN: 4806

European-Finnish (FIN) AF: 0.484 AC: 5090 AN: 10510

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.504 AC: 34221 AN: 67950

Other (OTH) AF: 0.548 AC: 1157 AN: 2110

Alfa AF: 0.515 Hom.: 68872

Bravo AF: 0.537

Asia WGS AF: 0.661 AC: 2297 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.3
DANN	Benign	0.57
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs869714; hg19: chr1-167126250;