19-30009211-GTGATGATGATGATGA-GTGATGATGA

Position:

• chr19-30009211-GTGATGATGATGATGA-GTGATGATGA

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_003796.3(URI1):​c.915_920delTGATGA​(p.Asp306_Asp307del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.00296 in 1,445,066 control chromosomes in the GnomAD database, including 9 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0018 (2 hom., cov: 0)
  • Exomes 𝑓: 0.0031 (7 hom.)
• Consequence: URI1 NM_003796.3 disruptive_inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.36

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 Likely_benign. Variant got -4 ACMG points.

• BS2: High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
URI1	NM_003796.3	c.915_920delTGATGA	p.Asp306_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.915_920delTGATGA	p.Asp306_Asp307del	disruptive_inframe_deletion	8/11	1	NM_003796.3	ENSP00000376097.2

Frequencies

GnomAD3 genomes AF: 0.00182 AC: 274 AN: 150588 Hom.: 2 Cov.: 0

Gnomad AFR AF: 0.000831

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00172

Gnomad ASJ AF: 0.00579

Gnomad EAS AF: 0.000392

Gnomad SAS AF: 0.000421

Gnomad FIN AF: 0.000965

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00256

Gnomad OTH AF: 0.00341

GnomAD3 exomes AF: 0.00451 AC: 953 AN: 211522 Hom.: 2 AF XY: 0.00438 AC XY: 498 AN XY: 113756

Gnomad AFR exome AF: 0.00159

Gnomad AMR exome AF: 0.00353

Gnomad ASJ exome AF: 0.00763

Gnomad EAS exome AF: 0.00187

Gnomad SAS exome AF: 0.00178

Gnomad FIN exome AF: 0.00574

Gnomad NFE exome AF: 0.00587

Gnomad OTH exome AF: 0.00554

GnomAD4 exome AF: 0.00309 AC: 3998 AN: 1294358 Hom.: 7 AF XY: 0.00297 AC XY: 1909 AN XY: 643664

Gnomad4 AFR exome AF: 0.000662

Gnomad4 AMR exome AF: 0.00308

Gnomad4 ASJ exome AF: 0.00647

Gnomad4 EAS exome AF: 0.00141

Gnomad4 SAS exome AF: 0.000700

Gnomad4 FIN exome AF: 0.00349

Gnomad4 NFE exome AF: 0.00334

Gnomad4 OTH exome AF: 0.00293

GnomAD4 genome AF: 0.00182 AC: 274 AN: 150708 Hom.: 2 Cov.: 0 AF XY: 0.00178 AC XY: 131 AN XY: 73564

Gnomad4 AFR AF: 0.000829

Gnomad4 AMR AF: 0.00172

Gnomad4 ASJ AF: 0.00579

Gnomad4 EAS AF: 0.000392

Gnomad4 SAS AF: 0.000422

Gnomad4 FIN AF: 0.000965

Gnomad4 NFE AF: 0.00256

Gnomad4 OTH AF: 0.00338

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;