rs1800624

Variant names:

• chr6-32184610-A-G
• rs1800624
• NM_002586.5:c.*1772T>C

Your query was ambiguous. Multiple possible variants found:

• chr6-32184610-A-G
• chr6-32184610-A-T

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.*1772T>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000141 in 142,288 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000014 (0 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PBX2 NM_002586.5 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.213
• Publications: 217 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=-0.81).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PBX2	NM_002586.5	c.*1772T>C		downstream_gene_variant		ENST00000375050.6	NP_002577.2
PBX2	XM_047418839.1	c.*1772T>C		downstream_gene_variant			XP_047274795.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PBX2	ENST00000375050.6	c.*1772T>C		downstream_gene_variant		1	NM_002586.5	ENSP00000364190.3
ENSG00000273333	ENST00000559458.2	n.*123T>C		downstream_gene_variant		2

Frequencies

GnomAD3 genomes AF: 0.0000141 AC: 2 AN: 142288 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000296

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 122082 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 61136

African (AFR) AF: 0.00 AC: 0 AN: 3586

American (AMR) AF: 0.00 AC: 0 AN: 3898

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 5200

East Asian (EAS) AF: 0.00 AC: 0 AN: 10692

South Asian (SAS) AF: 0.00 AC: 0 AN: 2264

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 7310

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 654

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 79952

Other (OTH) AF: 0.00 AC: 0 AN: 8526

GnomAD4 genome AF: 0.0000141 AC: 2 AN: 142288 Hom.: 0 Cov.: 33 AF XY: 0.0000144 AC XY: 1 AN XY: 69530

African (AFR) AF: 0.00 AC: 0 AN: 33570

American (AMR) AF: 0.00 AC: 0 AN: 14564

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3382

East Asian (EAS) AF: 0.00 AC: 0 AN: 4886

South Asian (SAS) AF: 0.00 AC: 0 AN: 4614

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10566

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 310

European-Non Finnish (NFE) AF: 0.0000296 AC: 2 AN: 67536

Other (OTH) AF: 0.00 AC: 0 AN: 1956

Alfa AF: 0.00 Hom.: 186

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.9
DANN	Benign	0.68
PhyloP100		0.21
PromoterAI		0.0079	Neutral

Splicing

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

Other links and lift over

dbSNP: rs1800624; hg19: chr6-32152387;