rs10814079

Positions:

• chr9-34226089-G-C
• chr9-34226089-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_016525.5(UBAP1):​c.34+5141G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.359 in 141,696 control chromosomes in the GnomAD database, including 9,584 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.36 (9584 hom., cov: 27)
• Consequence: UBAP1 NM_016525.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.718 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UBAP1	NM_016525.5	c.34+5141G>C		intron_variant		ENST00000297661.9	NP_057609.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UBAP1	ENST00000297661.9	c.34+5141G>C		intron_variant		1	NM_016525.5	ENSP00000297661	P1

Frequencies

GnomAD3 genomes AF: 0.359 AC: 50795 AN: 141578 Hom.: 9571 Cov.: 27

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.738

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.486

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.377

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.359 AC: 50839 AN: 141696 Hom.: 9584 Cov.: 27 AF XY: 0.368 AC XY: 25330 AN XY: 68886

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.419

Gnomad4 ASJ AF: 0.354

Gnomad4 EAS AF: 0.738

Gnomad4 SAS AF: 0.544

Gnomad4 FIN AF: 0.375

Gnomad4 NFE AF: 0.354

Gnomad4 OTH AF: 0.382

Alfa AF: 0.195 Hom.: 399

Bravo AF: 0.341

Asia WGS AF: 0.567 AC: 1900 AN: 3366

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.74

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: rs10814079; hg19: chr9-34226087; COSMIC: COSV52661527; COSMIC: COSV52661527;