12-109543873-C-T

Variant summary

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

The XM_011538961.2(UBE3B):c.*260C>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 0.567 in 151,772 control chromosomes in the GnomAD database, including 25,410 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 0.57 (25410 hom., cov: 29)
• Consequence: UBE3B XM_011538961.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.668

Genes affected

UBE3B (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UBE3B	XM_011538961.2	c.*260C>T		3_prime_UTR_variant	28/28
UBE3B	XM_047429851.1	c.*260C>T		3_prime_UTR_variant	28/28
UBE3B	XM_047429852.1	c.*260C>T		3_prime_UTR_variant	28/28

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.567 AC: 85953 AN: 151658 Hom.: 25369 Cov.: 29

Gnomad AFR AF: 0.723

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.567 AC: 86055 AN: 151772 Hom.: 25410 Cov.: 29 AF XY: 0.557 AC XY: 41308 AN XY: 74168

Gnomad4 AFR AF: 0.724

Gnomad4 AMR AF: 0.503

Gnomad4 ASJ AF: 0.532

Gnomad4 EAS AF: 0.297

Gnomad4 SAS AF: 0.388

Gnomad4 FIN AF: 0.464

Gnomad4 NFE AF: 0.536

Gnomad4 OTH AF: 0.581

Alfa AF: 0.506 Hom.: 2622

Bravo AF: 0.581

Asia WGS AF: 0.383 AC: 1332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.91
Dann	Benign	0.12

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs731178; hg19: chr12-109981678; COSMIC: COSV50457784;