19-30009211-GTGATGATGATGATGA-GTGATGA

Position:

• chr19-30009211-GTGATGATGATGATGA-GTGATGA

Variant summary

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

The NM_003796.3(URI1):​c.912_920delTGATGATGA​(p.Asp305_Asp307del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.0000409 in 1,541,270 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: 𝑓 0.00010 (0 hom., cov: 0)
  • Exomes 𝑓: 0.000035 (0 hom.)
• Consequence: URI1 NM_003796.3 disruptive_inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.01

Genes affected

URI1 (HGNC:13236): (URI1 prefoldin like chaperone) This gene encodes member of the prefoldin family of molecular chaperones. The encoded protein functions as a scaffolding protein and plays roles in ubiquitination and transcription, in part though interactions with the RNA polymerase II subunit RPB5. This gene may play a role in multiple malignancies including ovarian cancer and hepatocellular carcinoma. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and a pseudogene of this gene is located on the long arm of chromosome 22. [provided by RefSeq, Nov 2011]

URI1 (HGNC:):

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	Protein	UniProt
URI1	NM_003796.3	c.912_920delTGATGATGA	p.Asp305_Asp307del	disruptive_inframe_deletion	8/11	ENST00000392271.6	NP_003787.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
URI1	ENST00000392271.6	c.912_920delTGATGATGA	p.Asp305_Asp307del	disruptive_inframe_deletion	8/11	1	NM_003796.3	ENSP00000376097.2

Frequencies

GnomAD3 genomes AF: 0.0000995 AC: 15 AN: 150686 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0000734

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000211

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000162

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000520 AC: 11 AN: 211522 Hom.: 0 AF XY: 0.0000615 AC XY: 7 AN XY: 113756

Gnomad AFR exome AF: 0.0000693

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.0000644

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000958

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000345 AC: 48 AN: 1390584 Hom.: 0 AF XY: 0.0000347 AC XY: 24 AN XY: 692106

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.0000401

Gnomad4 EAS exome AF: 0.0000785

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000398

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0000995 AC: 15 AN: 150686 Hom.: 0 Cov.: 0 AF XY: 0.000122 AC XY: 9 AN XY: 73480

Gnomad4 AFR AF: 0.0000734

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000211

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000162

Gnomad4 OTH AF: 0.00

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: rs3840928; hg19: chr19-30500118;