rs61003310

Variant names:

• chr12-56116165-GAA-G
• rs61003310
• ENST00000870200.1:c.*372_*373delAA

Your query was ambiguous. Multiple possible variants found:

• chr12-56116165-GAA-G
• chr12-56116165-GAA-GA
• chr12-56116165-GAA-GAAA

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The ENST00000870200.1(PA2G4):​c.*372_*373delAA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000139 in 143,906 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 0)
  • Exomes 𝑓: 0.000014 (0 hom.)
• Consequence: PA2G4 ENST00000870200.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610
• Publications: 0 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 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

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.*372_*373delAA		3_prime_UTR	Exon 14 of 14	ENSP00000540259.1
	ENSG00000258317	ENST00000716007.1		n.756+331_756+332delTT		intron	N/A
	ENSG00000258317	ENST00000732776.1		n.905+331_905+332delTT		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome AF: 0.0000139 AC: 2 AN: 143906 Hom.: 0 AF XY: 0.0000233 AC XY: 2 AN XY: 85818

African (AFR) AF: 0.00 AC: 0 AN: 3452

American (AMR) AF: 0.00 AC: 0 AN: 13956

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 5700

East Asian (EAS) AF: 0.00 AC: 0 AN: 4626

South Asian (SAS) AF: 0.0000361 AC: 1 AN: 27668

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 5834

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 510

European-Non Finnish (NFE) AF: 0.0000132 AC: 1 AN: 75930

Other (OTH) AF: 0.00 AC: 0 AN: 6230

GnomAD4 genome Cov.: 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;