Genetic Variant URI1:p.Asp305_Asp307del (chr19-30009211-GTGATGATGA-G) – ACMG Classification: Uncertain_significance (1 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2BP3

The NM_003796.3(URI1):c.912_920delTGATGATGA(p.Asp305_Asp307del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.0000409 in 1,541,270 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00010 ( 0 hom., cov: 0)

Exomes 𝑓: 0.000035 ( 0 hom. )

Consequence

URI1
NM_003796.3 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 7.01

Publications

17 publications found

Variant links:

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 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

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

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
URI1	NM_003796.3	MANE Select	c.912_920delTGATGATGA	p.Asp305_Asp307del	disruptive_inframe_deletion	Exon 8 of 11	NP_003787.2	O94763-1
URI1	NM_001252641.2		c.858_866delTGATGATGA	p.Asp287_Asp289del	disruptive_inframe_deletion	Exon 8 of 11	NP_001239570.1	O94763-4
URI1	NR_045557.1		n.1186_1194delTGATGATGA		non_coding_transcript_exon	Exon 7 of 10

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
URI1	ENST00000392271.6	TSL:1 MANE Select	c.912_920delTGATGATGA	p.Asp305_Asp307del	disruptive_inframe_deletion	Exon 8 of 11	ENSP00000376097.2	O94763-1
URI1	ENST00000360605.8	TSL:1	c.858_866delTGATGATGA	p.Asp287_Asp289del	disruptive_inframe_deletion	Exon 8 of 11	ENSP00000353817.4	O94763-4
URI1	ENST00000574110.5	TSL:1	n.745_753delTGATGATGA		non_coding_transcript_exon	Exon 7 of 10	ENSP00000461003.1	I3L467

Frequencies

GnomAD3 genomes

AF:

0.0000995

AC:

AN:

150686

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000734

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000211

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000162

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.0000520

AC:

AN:

211522

AF XY:

0.0000615

show subpopulations

Gnomad AFR exome

AF:

0.0000693

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0000644

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000958

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000345

AC:

AN:

1390584

Hom.:

AF XY:

0.0000347

AC XY:

AN XY:

692106

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

32770

American (AMR)

AF:

0.00

AC:

AN:

42882

Ashkenazi Jewish (ASJ)

AF:

0.0000401

AC:

AN:

24930

East Asian (EAS)

AF:

0.0000785

AC:

AN:

38196

South Asian (SAS)

AF:

0.00

AC:

AN:

82514

European-Finnish (FIN)

AF:

0.00

AC:

AN:

50288

Middle Eastern (MID)

AF:

0.000357

AC:

AN:

5604

European-Non Finnish (NFE)

AF:

0.0000398

AC:

AN:

1055764

Other (OTH)

AF:

0.00

AC:

AN:

57636

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.483

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0000995

AC:

AN:

150686

Hom.:

Cov.:

AF XY:

0.000122

AC XY:

AN XY:

73480

show subpopulations

African (AFR)

AF:

0.0000734

AC:

AN:

40896

American (AMR)

AF:

0.00

AC:

AN:

15106

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3456

East Asian (EAS)

AF:

0.00

AC:

AN:

5108

South Asian (SAS)

AF:

0.000211

AC:

AN:

4748

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10404

Middle Eastern (MID)

AF:

0.00

AC:

AN:

316

European-Non Finnish (NFE)

AF:

0.000162

AC:

AN:

67696

Other (OTH)

AF:

0.00

AC:

AN:

2054

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0000614

Hom.:

4812

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

7.0

Mutation Taster

=98/102

disease causing

(source)

Splicing

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

Publications

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19-30009211-GTGATGATGATGATGA-GTGATGA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over