rs750397204

chr5-140114295-GGGCGGCGGCGGCAGTGGCGGCGGCGGC-Gchr5-140114295-GGGCGGCGGCGGCAGTGGCGGCGGCGGC-GGGCchr5-140114295-GGGCGGCGGCGGCAGTGGCGGCGGCGGC-GGGCGGCchr5-140114295-GGGCGGCGGCGGCAGTGGCGGCGGCGGC-GGGCGGCGGCGGCAGTGGCGGCGGCGGCGGCGGCAGTGGCGGCGGCGGC

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_005859.5(PURA):c.120_146del(p.Gly41_Gly49del) variant causes a inframe deletion change. The variant allele was found at a frequency of 0.00000271 in 1,105,442 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. G39G) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 31)
  • Exomes 𝑓: 0.0000027 (0 hom.)
• Consequence: PURA NM_005859.5 inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.66

Genes affected

PURA (HGNC:9701): (purine rich element binding protein A) This gene product is a sequence-specific, single-stranded DNA-binding protein. It binds preferentially to the single strand of the purine-rich element termed PUR, which is present at origins of replication and in gene flanking regions in a variety of eukaryotes from yeasts through humans. Thus, it is implicated in the control of both DNA replication and transcription. Deletion of this gene has been associated with myelodysplastic syndrome and acute myelogenous leukemia. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PURA	NM_005859.5	c.120_146del	p.Gly41_Gly49del	inframe_deletion	1/1	ENST00000331327.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PURA	ENST00000331327.5	c.120_146del	p.Gly41_Gly49del	inframe_deletion	1/1		NM_005859.5	P1
PURA	ENST00000505703.2	c.120_146del	p.Gly41_Gly49del	inframe_deletion	2/2	3
PURA	ENST00000651386.1	c.120_146del	p.Gly41_Gly49del	inframe_deletion	2/2			P1
PURA	ENST00000502351.1			downstream_gene_variant		2

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD3 exomes AF: 0.000140 AC: 1 AN: 7138 Hom.: 0 AF XY: 0.000220 AC XY: 1 AN XY: 4552

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00301

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000271 AC: 3 AN: 1105442 Hom.: 0 AF XY: 0.00000376 AC XY: 2 AN XY: 531434

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.0000715

Gnomad4 EAS exome AF: 0.0000387

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000106

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 31

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs750397204; hg19: chr5-139493880;