chr19-30009211-GTGA-G

Position:

• chr19-30009211-GTGA-G

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6 BA1

The NM_003796.3(URI1):​c.918_920del​(p.Asp311del) variant causes a inframe deletion change. The variant allele was found at a frequency of 0.83 in 1,540,862 control chromosomes in the GnomAD database, including 526,078 homozygotes. Variant has been reported in Lovd as Benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.80 (49457 hom., cov: 0)
  • Exomes 𝑓: 0.83 (476621 hom.)
• Consequence: URI1 NM_003796.3 inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.71

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]

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP6: Variant 19-30009211-GTGA-G is Benign according to our data. Variant chr19-30009211-GTGA-G is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
URI1	NM_003796.3	c.918_920del	p.Asp311del	inframe_deletion	8/11	ENST00000392271.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
URI1	ENST00000392271.6	c.918_920del	p.Asp311del	inframe_deletion	8/11	1	NM_003796.3	P2
URI1	ENST00000360605.8	c.864_866del	p.Asp293del	inframe_deletion	8/11	1		A2
URI1	ENST00000574110.5	c.*751_*753del		3_prime_UTR_variant, NMD_transcript_variant	7/10	1
URI1	ENST00000575242.1	c.157_159del	p.Asp58del	inframe_deletion	1/3	2

Frequencies

GnomAD3 genomes AF: 0.799 AC: 120298 AN: 150586 Hom.: 49436 Cov.: 0

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.981

Gnomad AMR AF: 0.816

Gnomad ASJ AF: 0.889

Gnomad EAS AF: 0.750

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.915

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.895

Gnomad OTH AF: 0.826

GnomAD3 exomes AF: 0.818 AC: 173110 AN: 211522 Hom.: 70586 AF XY: 0.825 AC XY: 93861 AN XY: 113756

Gnomad AFR exome AF: 0.576

Gnomad AMR exome AF: 0.768

Gnomad ASJ exome AF: 0.878

Gnomad EAS exome AF: 0.712

Gnomad SAS exome AF: 0.803

Gnomad FIN exome AF: 0.897

Gnomad NFE exome AF: 0.872

Gnomad OTH exome AF: 0.833

GnomAD4 exome AF: 0.833 AC: 1158550 AN: 1390154 Hom.: 476621 AF XY: 0.832 AC XY: 575897 AN XY: 691856

Gnomad4 AFR exome AF: 0.559

Gnomad4 AMR exome AF: 0.748

Gnomad4 ASJ exome AF: 0.841

Gnomad4 EAS exome AF: 0.742

Gnomad4 SAS exome AF: 0.777

Gnomad4 FIN exome AF: 0.860

Gnomad4 NFE exome AF: 0.853

Gnomad4 OTH exome AF: 0.809

GnomAD4 genome AF: 0.799 AC: 120352 AN: 150708 Hom.: 49457 Cov.: 0 AF XY: 0.800 AC XY: 58866 AN XY: 73558

Gnomad4 AFR AF: 0.593

Gnomad4 AMR AF: 0.816

Gnomad4 ASJ AF: 0.889

Gnomad4 EAS AF: 0.751

Gnomad4 SAS AF: 0.832

Gnomad4 FIN AF: 0.915

Gnomad4 NFE AF: 0.895

Gnomad4 OTH AF: 0.825

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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;