rs7527143

Variant names:

• chr1-167158117-G-A
• rs7527143
• ENST00000632571.1:c.-282+8166C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-167158117-G-A
• chr1-167158117-G-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000632571.1(GPA33):​c.-282+8166C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.531 in 151,000 control chromosomes in the GnomAD database, including 21,459 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 (21459 hom., cov: 31)
• Consequence: GPA33 ENST00000632571.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.667 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPA33	ENST00000632571.1	c.-282+8166C>T		intron_variant	Intron 1 of 3	4		ENSP00000488407.1

Frequencies

GnomAD3 genomes AF: 0.531 AC: 80051 AN: 150884 Hom.: 21426 Cov.: 31

Gnomad AFR AF: 0.528

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.686

Gnomad SAS AF: 0.653

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.551

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

GnomAD4 genome AF: 0.531 AC: 80125 AN: 151000 Hom.: 21459 Cov.: 31 AF XY: 0.533 AC XY: 39339 AN XY: 73752

Gnomad4 AFR AF: 0.528

Gnomad4 AMR AF: 0.586

Gnomad4 ASJ AF: 0.553

Gnomad4 EAS AF: 0.686

Gnomad4 SAS AF: 0.654

Gnomad4 FIN AF: 0.488

Gnomad4 NFE AF: 0.503

Gnomad4 OTH AF: 0.552

Alfa AF: 0.516 Hom.: 9666

Bravo AF: 0.536

Asia WGS AF: 0.661 AC: 2298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	12
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7527143; hg19: chr1-167127354;