Variant chr9-34220857-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_016525.5(UBAP1):c.-7-51G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 1,543,104 control chromosomes in the GnomAD database, including 20,651 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.12 ( 1527 hom., cov: 29)

Exomes 𝑓: 0.16 ( 19124 hom. )

Consequence

UBAP1
NM_016525.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.371

Variant links:

Genes affected

UBAP1 (HGNC:12461): (ubiquitin associated protein 1) This gene is a member of the UBA domain family, whose members include proteins having connections to ubiquitin and the ubiquitination pathway. The ubiquitin associated domain is thought to be a non-covalent ubiquitin binding domain consisting of a compact three helix bundle. This particular protein originates from a gene locus in a refined region on chromosome 9 undergoing loss of heterozygosity in nasopharyngeal carcinoma (NPC). Taking into account its cytogenetic location, this UBA domain family member is being studies as a putative target for mutation in nasopharyngeal carcinomas. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2010]

UBAP1 links:

UBAP1 (HGNC:):

UBAP1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 9-34220857-G-A is Benign according to our data. Variant chr9-34220857-G-A is described in ClinVar as [Benign]. Clinvar id is 1248653.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UBAP1	NM_016525.5 linkuse as main transcript	c.-7-51G>A		intron_variant		ENST00000297661.9	NP_057609.2	Q9NZ09-1A0A6G6AA68

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UBAP1	ENST00000297661.9 linkuse as main transcript	c.-7-51G>A		intron_variant		1	NM_016525.5	ENSP00000297661.4		Q9NZ09-1

Frequencies

GnomAD3 genomes

AF:

0.124

AC:

18833

AN:

151854

Hom.:

1527

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0339

Gnomad AMI

AF:

0.203

Gnomad AMR

AF:

0.132

Gnomad ASJ

AF:

0.162

Gnomad EAS

AF:

0.00637

Gnomad SAS

AF:

0.0638

Gnomad FIN

AF:

0.173

Gnomad MID

AF:

0.118

Gnomad NFE

AF:

0.180

Gnomad OTH

AF:

0.129

GnomAD4 exome

AF:

0.158

AC:

220218

AN:

1391132

Hom.:

19124

Cov.:

AF XY:

0.156

AC XY:

108679

AN XY:

695520

show subpopulations

Gnomad4 AFR exome

AF:

0.0260

Gnomad4 AMR exome

AF:

0.107

Gnomad4 ASJ exome

AF:

0.161

Gnomad4 EAS exome

AF:

0.00571

Gnomad4 SAS exome

AF:

0.0695

Gnomad4 FIN exome

AF:

0.171

Gnomad4 NFE exome

AF:

0.177

Gnomad4 OTH exome

AF:

0.147

GnomAD4 genome

AF:

0.124

AC:

18822

AN:

151972

Hom.:

1527

Cov.:

AF XY:

0.120

AC XY:

8945

AN XY:

74252

show subpopulations

Gnomad4 AFR

AF:

0.0338

Gnomad4 AMR

AF:

0.132

Gnomad4 ASJ

AF:

0.162

Gnomad4 EAS

AF:

0.00619

Gnomad4 SAS

AF:

0.0630

Gnomad4 FIN

AF:

0.173

Gnomad4 NFE

AF:

0.180

Gnomad4 OTH

AF:

0.127

Alfa

AF:

0.146

Hom.:

231

Bravo

AF:

0.116

Asia WGS

AF:

0.0340

AC:

120

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 17, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

1.3

DANN

Benign

0.75

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over