9-34251954-G-T

Position:

• chr9-34251954-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.*422G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 161,796 control chromosomes in the GnomAD database, including 2,474 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 0.16 (2352 hom., cov: 32)
  • Exomes 𝑓: 0.14 (122 hom.)
• Consequence: UBAP1 NM_016525.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UBAP1	NM_016525.5	c.*422G>T		3_prime_UTR_variant	7/7	ENST00000297661.9	NP_057609.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UBAP1	ENST00000297661.9	c.*422G>T		3_prime_UTR_variant	7/7	1	NM_016525.5	ENSP00000297661.4
UBAP1	ENST00000359544.2	c.*422G>T		3_prime_UTR_variant	7/7	1		ENSP00000352541.2
UBAP1	ENST00000379186.8	c.*422G>T		3_prime_UTR_variant	6/6	5		ENSP00000368484.3

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24185 AN: 151976 Hom.: 2349 Cov.: 32

Gnomad AFR AF: 0.0685

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.0532

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.168

GnomAD4 exome AF: 0.137 AC: 1329 AN: 9702 Hom.: 122 Cov.: 0 AF XY: 0.140 AC XY: 709 AN XY: 5072

Gnomad4 AFR exome AF: 0.0243

Gnomad4 AMR exome AF: 0.134

Gnomad4 ASJ exome AF: 0.104

Gnomad4 EAS exome AF: 0.0250

Gnomad4 SAS exome AF: 0.178

Gnomad4 FIN exome AF: 0.155

Gnomad4 NFE exome AF: 0.152

Gnomad4 OTH exome AF: 0.114

GnomAD4 genome AF: 0.159 AC: 24188 AN: 152094 Hom.: 2352 Cov.: 32 AF XY: 0.160 AC XY: 11864 AN XY: 74340

Gnomad4 AFR AF: 0.0683

Gnomad4 AMR AF: 0.162

Gnomad4 ASJ AF: 0.145

Gnomad4 EAS AF: 0.0535

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.187

Gnomad4 NFE AF: 0.211

Gnomad4 OTH AF: 0.167

Alfa AF: 0.169 Hom.: 994

Bravo AF: 0.149

Asia WGS AF: 0.149 AC: 520 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	9.4
DANN	Benign	0.63

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: rs3135929; hg19: chr9-34251952; COSMIC: COSV52662118; COSMIC: COSV52662118;