chr12-56116165-GA-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000870200.1(PA2G4):​c.*373delA 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 0.14 (828 hom., cov: 17)
  • Exomes 𝑓: 0.039 (241 hom.)
• 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: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

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.*373delA		3_prime_UTR	Exon 14 of 14	ENSP00000540259.1
	ENSG00000258317	ENST00000716007.1		n.756+332delT		intron	N/A
	ENSG00000258317	ENST00000732776.1		n.905+332delT		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.143 AC: 12681 AN: 88420 Hom.: 827 Cov.: 17

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.0913

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0836

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.0979

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.108

GnomAD2 exomes AF: 0.00371 AC: 210 AN: 56562 AF XY: 0.00365

Gnomad AFR exome AF: 0.0249

Gnomad AMR exome AF: 0.00458

Gnomad ASJ exome AF: 0.00365

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00282

Gnomad NFE exome AF: 0.00298

Gnomad OTH exome AF: 0.00426

GnomAD4 exome AF: 0.0385 AC: 5517 AN: 143224 Hom.: 241 Cov.: 0 AF XY: 0.0360 AC XY: 3078 AN XY: 85412

African (AFR) AF: 0.143 AC: 488 AN: 3408

American (AMR) AF: 0.0272 AC: 378 AN: 13920

Ashkenazi Jewish (ASJ) AF: 0.0217 AC: 123 AN: 5680

East Asian (EAS) AF: 0.00130 AC: 6 AN: 4624

South Asian (SAS) AF: 0.0414 AC: 1142 AN: 27580

European-Finnish (FIN) AF: 0.0461 AC: 268 AN: 5816

Middle Eastern (MID) AF: 0.0340 AC: 17 AN: 500

European-Non Finnish (NFE) AF: 0.0377 AC: 2843 AN: 75510

Other (OTH) AF: 0.0407 AC: 252 AN: 6186

GnomAD4 genome AF: 0.143 AC: 12691 AN: 88508 Hom.: 828 Cov.: 17 AF XY: 0.144 AC XY: 6023 AN XY: 41862

African (AFR) AF: 0.248 AC: 6144 AN: 24760

American (AMR) AF: 0.0910 AC: 701 AN: 7702

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 276 AN: 2230

East Asian (EAS) AF: 0.00154 AC: 5 AN: 3238

South Asian (SAS) AF: 0.0841 AC: 209 AN: 2486

European-Finnish (FIN) AF: 0.137 AC: 690 AN: 5042

Middle Eastern (MID) AF: 0.102 AC: 18 AN: 176

European-Non Finnish (NFE) AF: 0.108 AC: 4458 AN: 41236

Other (OTH) AF: 0.107 AC: 116 AN: 1088

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;