6-32186109-C-T

Variant names:

• chr6-32186109-C-T
• rs999
• NM_002586.5:c.*273G>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_002586.5(PBX2):​c.*273G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
  • Exomes 𝑓: 0.0000030 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PBX2 NM_002586.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 0 publications found

Genes affected

PBX2 (HGNC:8633): (PBX homeobox 2) This gene encodes a ubiquitously expressed member of the TALE/PBX homeobox family. It was identified by its similarity to a homeobox gene which is involved in t(1;19) translocation in acute pre-B-cell leukemias. This protein is a transcriptional activator which binds to the TLX1 promoter. The gene is located within the major histocompatibility complex (MHC) on chromosome 6. [provided by RefSeq, Jul 2008]

ENSG00000273333 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002586.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PBX2	NM_002586.5	MANE Select	c.*273G>A		3_prime_UTR	Exon 9 of 9	NP_002577.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PBX2	ENST00000375050.6	TSL:1 MANE Select	c.*273G>A		3_prime_UTR	Exon 9 of 9	ENSP00000364190.3
	ENSG00000273333	ENST00000559458.2	TSL:2	n.-227G>A		upstream_gene	N/A
	PBX2	ENST00000495300.1	TSL:3	n.*147G>A		downstream_gene	N/A

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000304 AC: 1 AN: 328428 Hom.: 0 Cov.: 0 AF XY: 0.00000587 AC XY: 1 AN XY: 170254

African (AFR) AF: 0.00 AC: 0 AN: 9562

American (AMR) AF: 0.00 AC: 0 AN: 11632

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 11050

East Asian (EAS) AF: 0.00 AC: 0 AN: 25246

South Asian (SAS) AF: 0.00 AC: 0 AN: 23408

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 23660

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1532

European-Non Finnish (NFE) AF: 0.00000494 AC: 1 AN: 202234

Other (OTH) AF: 0.00 AC: 0 AN: 20104

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.0000189

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	11
DANN	Benign	0.83
PhyloP100		0.25
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		0.95

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs999; hg19: chr6-32153886;