Variant rs750397204 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_005859.5(PURA):c.120_146delCGGCGGCAGTGGCGGCGGCGGCGGCGG(p.Gly41_Gly49del) variant causes a disruptive 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.

Frequency

Genomes: not found (cov: 31)

Exomes 𝑓: 0.0000027 ( 0 hom. )

Consequence

PURA
NM_005859.5 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.66

Variant links:

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]

PURA links:

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ACMG classification

Classification made for transcript

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	Protein	UniProt
PURA	NM_005859.5 link	c.120_146delCGGCGGCAGTGGCGGCGGCGGCGGCGG	p.Gly41_Gly49del	disruptive_inframe_deletion	1/1	ENST00000331327.5	NP_005850.1	Q00577

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
PURA	ENST00000331327.5 link	c.120_146delCGGCGGCAGTGGCGGCGGCGGCGGCGG	p.Gly41_Gly49del	disruptive_inframe_deletion	1/1	6	NM_005859.5	ENSP00000332706.3	Q00577
PURA	ENST00000651386.1 link	c.120_146delCGGCGGCAGTGGCGGCGGCGGCGGCGG	p.Gly41_Gly49del	disruptive_inframe_deletion	2/2			ENSP00000499133.1	Q00577
PURA	ENST00000505703.2 link	c.120_146delCGGCGGCAGTGGCGGCGGCGGCGGCGG	p.Gly41_Gly49del	disruptive_inframe_deletion	2/2	3		ENSP00000498560.1	A0A494C0H6
PURA	ENST00000502351.1 link	c.36_62delGGCGGCGGCGGCAGTGGCGGCGGCGGC		downstream_gene_variant		2		ENSP00000498760.1	A0A494C0X8

Frequencies

GnomAD3 genomes

Cov.:

GnomAD3 exomes

AF:

0.000140

AC:

AN:

7138

Hom.:

AF XY:

0.000220

AC XY:

AN XY:

4552

show subpopulations

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:

AN:

1105442

Hom.:

AF XY:

0.00000376

AC XY:

AN XY:

531434

show subpopulations

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.:

Bravo

AF:

0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over