rs28927680

Positions:

• chr11-116748357-C-G
• chr11-116748357-C-T

Variant summary

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

The ENST00000260210.5(BUD13):​c.*125G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0739 in 771,744 control chromosomes in the GnomAD database, including 2,683 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 0.099 (935 hom., cov: 32)
  • Exomes 𝑓: 0.068 (1748 hom.)
• Consequence: BUD13 ENST00000260210.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.735

Genes affected

BUD13 (HGNC:28199): (BUD13 homolog) Enables RNA binding activity. Involved in mRNA splicing, via spliceosome. Located in nucleoplasm. Part of U2-type precatalytic spliceosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BUD13	NM_032725.4	c.*125G>C		3_prime_UTR_variant	10/10	ENST00000260210.5	NP_116114.1
BUD13	NM_001159736.2	c.*125G>C		3_prime_UTR_variant	10/10		NP_001153208.1
BUD13	XM_011543035.3	c.*125G>C		3_prime_UTR_variant	10/10		XP_011541337.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BUD13	ENST00000260210.5	c.*125G>C		3_prime_UTR_variant	10/10	1	NM_032725.4	ENSP00000260210	P2
BUD13	ENST00000375445.7	c.*125G>C		3_prime_UTR_variant	10/10	1		ENSP00000364594	A2
BUD13	ENST00000419189.1	c.*405G>C		3_prime_UTR_variant, NMD_transcript_variant	4/4	5		ENSP00000415748

Frequencies

GnomAD3 genomes AF: 0.0985 AC: 14979 AN: 152120 Hom.: 931 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.0738

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.0476

Gnomad FIN AF: 0.0601

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0683

Gnomad OTH AF: 0.105

GnomAD4 exome AF: 0.0678 AC: 42000 AN: 619506 Hom.: 1748 Cov.: 8 AF XY: 0.0662 AC XY: 21410 AN XY: 323412

Gnomad4 AFR exome AF: 0.161

Gnomad4 AMR exome AF: 0.147

Gnomad4 ASJ exome AF: 0.0696

Gnomad4 EAS exome AF: 0.000746

Gnomad4 SAS exome AF: 0.0455

Gnomad4 FIN exome AF: 0.0682

Gnomad4 NFE exome AF: 0.0666

Gnomad4 OTH exome AF: 0.0752

GnomAD4 genome AF: 0.0986 AC: 15013 AN: 152238 Hom.: 935 Cov.: 32 AF XY: 0.0978 AC XY: 7278 AN XY: 74454

Gnomad4 AFR AF: 0.167

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.0738

Gnomad4 EAS AF: 0.000771

Gnomad4 SAS AF: 0.0478

Gnomad4 FIN AF: 0.0601

Gnomad4 NFE AF: 0.0684

Gnomad4 OTH AF: 0.104

Alfa AF: 0.0583 Hom.: 160

Bravo AF: 0.107

Asia WGS AF: 0.0420 AC: 146 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.1
DANN	Benign	0.73
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs28927680; hg19: chr11-116619073;