19-30009211-GTGATGATGATGATGA-GTGATGATGATGATGATGATGA

Variant names:

• chr19-30009211-G-GTGATGA
• rs3840928
• NM_003796.3:c.915_920dupTGATGA

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP3

The NM_003796.3(URI1):​c.915_920dupTGATGA​(p.Asp306_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. Synonymous variant affecting the same amino acid position (i.e. D307D) has been classified as Likely benign.

• Frequency:
  • Genomes: 𝑓 0.000040 (0 hom., cov: 0)
  • Exomes 𝑓: 0.000092 (0 hom.)
• Consequence: URI1 NM_003796.3 disruptive_inframe_insertion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.421
• Publications: 17 publications found

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

Our verdict: Likely_benign. The variant received -1 ACMG points.

• BP3: Nonframeshift variant in repetitive region in NM_003796.3

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003796.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	URI1	NM_003796.3	MANE Select	c.915_920dupTGATGA	p.Asp306_Asp307dup	disruptive_inframe_insertion	Exon 8 of 11	NP_003787.2	O94763-1
	URI1	NM_001252641.2		c.861_866dupTGATGA	p.Asp288_Asp289dup	disruptive_inframe_insertion	Exon 8 of 11	NP_001239570.1	O94763-4
	URI1	NR_045557.1		n.1189_1194dupTGATGA		non_coding_transcript_exon	Exon 7 of 10

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	URI1	ENST00000392271.6	TSL:1 MANE Select	c.915_920dupTGATGA	p.Asp306_Asp307dup	disruptive_inframe_insertion	Exon 8 of 11	ENSP00000376097.2	O94763-1
	URI1	ENST00000360605.8	TSL:1	c.861_866dupTGATGA	p.Asp288_Asp289dup	disruptive_inframe_insertion	Exon 8 of 11	ENSP00000353817.4	O94763-4
	URI1	ENST00000574110.5	TSL:1	n.*748_*753dupTGATGA		non_coding_transcript_exon	Exon 7 of 10	ENSP00000461003.1	I3L467

Frequencies

GnomAD3 genomes AF: 0.0000398 AC: 6 AN: 150686 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0000978

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000295

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.0000851 AC: 18 AN: 211522 AF XY: 0.0000527

Gnomad AFR exome AF: 0.000277

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.0000644

Gnomad FIN exome AF: 0.0000563

Gnomad NFE exome AF: 0.000128

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000920 AC: 128 AN: 1390742 Hom.: 0 Cov.: 0 AF XY: 0.0000795 AC XY: 55 AN XY: 692176

African (AFR) AF: 0.0000610 AC: 2 AN: 32770

American (AMR) AF: 0.00 AC: 0 AN: 42884

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 24930

East Asian (EAS) AF: 0.0000785 AC: 3 AN: 38196

South Asian (SAS) AF: 0.00 AC: 0 AN: 82518

European-Finnish (FIN) AF: 0.0000199 AC: 1 AN: 50318

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5604

European-Non Finnish (NFE) AF: 0.000115 AC: 121 AN: 1055886

Other (OTH) AF: 0.0000174 AC: 1 AN: 57636

GnomAD4 genome AF: 0.0000398 AC: 6 AN: 150686 Hom.: 0 Cov.: 0 AF XY: 0.0000544 AC XY: 4 AN XY: 73480

African (AFR) AF: 0.0000978 AC: 4 AN: 40896

American (AMR) AF: 0.00 AC: 0 AN: 15106

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3456

East Asian (EAS) AF: 0.00 AC: 0 AN: 5108

South Asian (SAS) AF: 0.00 AC: 0 AN: 4748

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10404

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.0000295 AC: 2 AN: 67696

Other (OTH) AF: 0.00 AC: 0 AN: 2054

Alfa AF: 0.00 Hom.: 4812

Bravo AF: 0.0000642

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.42
Mutation Taster		=77/23	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs3840928; hg19: chr19-30500118;