19-30009211-GTGATGATGATGATGA-GTGATGATGATGATGATGA

Position:

• chr19-30009211-GTGATGATGATGATGA-GTGATGATGATGATGATGA

Variant summary

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

The NM_003796.3(URI1):​c.918_920dupTGA​(p.Asp307dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0042 (4 hom., cov: 0)
  • Exomes 𝑓: 0.00060 (3 hom.)
• Consequence: URI1 NM_003796.3 disruptive_inframe_insertion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.421

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 4 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
URI1	NM_003796.3	c.918_920dupTGA	p.Asp307dup	disruptive_inframe_insertion	8/11	ENST00000392271.6	NP_003787.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
URI1	ENST00000392271.6	c.918_920dupTGA	p.Asp307dup	disruptive_inframe_insertion	8/11	1	NM_003796.3	ENSP00000376097.2

Frequencies

GnomAD3 genomes AF: 0.00416 AC: 627 AN: 150682 Hom.: 4 Cov.: 0

Gnomad AFR AF: 0.0141

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00225

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000196

Gnomad SAS AF: 0.000421

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.000133

Gnomad OTH AF: 0.00243

GnomAD3 exomes AF: 0.00168 AC: 355 AN: 211522 Hom.: 2 AF XY: 0.00132 AC XY: 150 AN XY: 113756

Gnomad AFR exome AF: 0.0179

Gnomad AMR exome AF: 0.00119

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.0000644

Gnomad SAS exome AF: 0.00110

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000298

Gnomad OTH exome AF: 0.000765

GnomAD4 exome AF: 0.000599 AC: 833 AN: 1390736 Hom.: 3 Cov.: 0 AF XY: 0.000582 AC XY: 403 AN XY: 692174

Gnomad4 AFR exome AF: 0.0139

Gnomad4 AMR exome AF: 0.00117

Gnomad4 ASJ exome AF: 0.0000401

Gnomad4 EAS exome AF: 0.000131

Gnomad4 SAS exome AF: 0.000897

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000171

Gnomad4 OTH exome AF: 0.00104

GnomAD4 genome AF: 0.00415 AC: 626 AN: 150802 Hom.: 4 Cov.: 0 AF XY: 0.00389 AC XY: 286 AN XY: 73606

Gnomad4 AFR AF: 0.0140

Gnomad4 AMR AF: 0.00225

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000196

Gnomad4 SAS AF: 0.000422

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000133

Gnomad4 OTH AF: 0.00241

Bravo AF: 0.00499

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;