12-56116165-GAA-GAAA

Variant names:

• chr12-56116165-G-GA
• rs61003310
• ENST00000870200.1:c.*373dupA

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The ENST00000870200.1(PA2G4):​c.*373dupA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.000011 (0 hom., cov: 17)
• Consequence: PA2G4 ENST00000870200.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610
• Publications: 1 publications found

Genes affected

PA2G4 (HGNC:8550): (proliferation-associated 2G4) This gene encodes an RNA-binding protein that is involved in growth regulation. This protein is present in pre-ribosomal ribonucleoprotein complexes and may be involved in ribosome assembly and the regulation of intermediate and late steps of rRNA processing. This protein can interact with the cytoplasmic domain of the ErbB3 receptor and may contribute to transducing growth regulatory signals. This protein is also a transcriptional co-repressor of androgen receptor-regulated genes and other cell cycle regulatory genes through its interactions with histone deacetylases. This protein has been implicated in growth inhibition and the induction of differentiation of human cancer cells. Six pseudogenes, located on chromosomes 3, 6, 9, 18, 20 and X, have been identified. [provided by RefSeq, Jul 2008]

ENSG00000258317 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000870200.1. 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
	PA2G4	ENST00000870200.1		c.*373dupA		3_prime_UTR	Exon 14 of 14	ENSP00000540259.1
	ENSG00000258317	ENST00000716007.1		n.756+332dupT		intron	N/A
	ENSG00000258317	ENST00000732776.1		n.905+332dupT		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0000112 AC: 1 AN: 89344 Hom.: 0 Cov.: 17

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000308

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Cov.: 0

GnomAD4 genome AF: 0.0000112 AC: 1 AN: 89344 Hom.: 0 Cov.: 17 AF XY: 0.0000237 AC XY: 1 AN XY: 42206

African (AFR) AF: 0.00 AC: 0 AN: 25002

American (AMR) AF: 0.00 AC: 0 AN: 7758

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2252

East Asian (EAS) AF: 0.000308 AC: 1 AN: 3246

South Asian (SAS) AF: 0.00 AC: 0 AN: 2498

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 5108

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 196

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 41650

Other (OTH) AF: 0.00 AC: 0 AN: 1074

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.061

Splicing

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

Other links and lift over

dbSNP: rs61003310; hg19: chr12-56509949;