20-12380707-C-T

Variant names:

• chr20-12380707-C-T
• rs6033392
• ENST00000414718.1:n.652C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000414718.1(PA2G4P2):​n.652C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0182 in 1,384,834 control chromosomes in the GnomAD database, including 429 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 0.033 (141 hom., cov: 32)
  • Exomes 𝑓: 0.016 (288 hom.)
• Consequence: PA2G4P2 ENST00000414718.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.59
• Publications: 1 publications found

Genes affected

PA2G4P2 (HGNC:16531): (proliferation-associated 2G4 pseudogene 2)

LOC124904870 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0695 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000414718.1. 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
	PA2G4P2	ENST00000414718.1	TSL:6	n.652C>T		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0327 AC: 4977 AN: 152094 Hom.: 141 Cov.: 32

Gnomad AFR AF: 0.0717

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0204

Gnomad ASJ AF: 0.0173

Gnomad EAS AF: 0.000387

Gnomad SAS AF: 0.0261

Gnomad FIN AF: 0.0169

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0187

Gnomad OTH AF: 0.0215

GnomAD4 exome AF: 0.0164 AC: 20171 AN: 1232622 Hom.: 288 Cov.: 21 AF XY: 0.0166 AC XY: 10341 AN XY: 624748

African (AFR) AF: 0.0679 AC: 1940 AN: 28560

American (AMR) AF: 0.0132 AC: 582 AN: 44178

Ashkenazi Jewish (ASJ) AF: 0.0130 AC: 319 AN: 24630

East Asian (EAS) AF: 0.000208 AC: 8 AN: 38524

South Asian (SAS) AF: 0.0224 AC: 1832 AN: 81610

European-Finnish (FIN) AF: 0.0150 AC: 793 AN: 52692

Middle Eastern (MID) AF: 0.0221 AC: 117 AN: 5288

European-Non Finnish (NFE) AF: 0.0151 AC: 13638 AN: 904762

Other (OTH) AF: 0.0180 AC: 942 AN: 52378

GnomAD4 genome AF: 0.0328 AC: 4986 AN: 152212 Hom.: 141 Cov.: 32 AF XY: 0.0325 AC XY: 2420 AN XY: 74428

African (AFR) AF: 0.0717 AC: 2976 AN: 41512

American (AMR) AF: 0.0203 AC: 311 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0173 AC: 60 AN: 3470

East Asian (EAS) AF: 0.000388 AC: 2 AN: 5158

South Asian (SAS) AF: 0.0261 AC: 126 AN: 4820

European-Finnish (FIN) AF: 0.0169 AC: 179 AN: 10618

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0187 AC: 1271 AN: 68024

Other (OTH) AF: 0.0213 AC: 45 AN: 2114

Alfa AF: 0.0263 Hom.: 7

Bravo AF: 0.0347

Asia WGS AF: 0.0210 AC: 72 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	11
DANN	Benign	0.89
PhyloP100		2.6

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6033392;

hg19: chr20-12361355;