rs3840928

Variant names:

• chr19-30009211-GTGATGATGATGATGA-G
• rs3840928
• NM_003796.3:c.906_920delTGATGATGATGATGA

Your query was ambiguous. Multiple possible variants found:

• chr19-30009211-GTGATGATGATGATGA-G
• chr19-30009211-GTGATGATGATGATGA-GTGA
• chr19-30009211-GTGATGATGATGATGA-GTGATGA
• chr19-30009211-GTGATGATGATGATGA-GTGATGATGA
• chr19-30009211-GTGATGATGATGATGA-GTGATGATGATGA
• chr19-30009211-GTGATGATGATGATGA-GTGATGATGATGATGATGA
• chr19-30009211-GTGATGATGATGATGA-GTGATGATGATGATGATGATGA
• chr19-30009211-GTGATGATGATGATGA-GTGATGATGATGATGATGATGATGA
• chr19-30009211-GTGATGATGATGATGA-GTGATGATGATGATGATGATGATGATGATGA

Variant summary

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

The NM_003796.3(URI1):​c.906_920delTGATGATGATGATGA​(p.Asp303_Asp307del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.00000288 in 1,390,742 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 0)
  • Exomes 𝑓: 0.0000029 (0 hom.)
• Consequence: URI1 NM_003796.3 disruptive_inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.01
• 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.906_920delTGATGATGATGATGA	p.Asp303_Asp307del	disruptive_inframe_deletion	Exon 8 of 11	NP_003787.2	O94763-1
	URI1	NM_001252641.2		c.852_866delTGATGATGATGATGA	p.Asp285_Asp289del	disruptive_inframe_deletion	Exon 8 of 11	NP_001239570.1	O94763-4
	URI1	NR_045557.1		n.1180_1194delTGATGATGATGATGA		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.906_920delTGATGATGATGATGA	p.Asp303_Asp307del	disruptive_inframe_deletion	Exon 8 of 11	ENSP00000376097.2	O94763-1
	URI1	ENST00000360605.8	TSL:1	c.852_866delTGATGATGATGATGA	p.Asp285_Asp289del	disruptive_inframe_deletion	Exon 8 of 11	ENSP00000353817.4	O94763-4
	URI1	ENST00000574110.5	TSL:1	n.*739_*753delTGATGATGATGATGA		non_coding_transcript_exon	Exon 7 of 10	ENSP00000461003.1	I3L467

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome AF: 0.00000288 AC: 4 AN: 1390742 Hom.: 0 AF XY: 0.00000144 AC XY: 1 AN XY: 692176

African (AFR) AF: 0.00 AC: 0 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: 0.00 AC: 0 AN: 38196

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

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 50318

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

European-Non Finnish (NFE) AF: 0.00000189 AC: 2 AN: 1055886

Other (OTH) AF: 0.0000347 AC: 2 AN: 57636

GnomAD4 genome Cov.: 0

Alfa AF: 0.00 Hom.: 4812

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		7.0
Mutation Taster		=96/104	disease causing (long InDel)

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;