rs180327

Variant names:

• chr11-116752943-C-T
• rs180327
• NM_032725.4:c.1766+4203G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032725.4(BUD13):​c.1766+4203G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.579 in 151,992 control chromosomes in the GnomAD database, including 25,872 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 0.58 (25872 hom., cov: 31)
• Consequence: BUD13 NM_032725.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86
• Publications: 24 publications found

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]

BUD13 Gene-Disease associations (from GenCC):

• progeroid syndrome

  Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

ENSG00000308823 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032725.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BUD13	NM_032725.4	MANE Select	c.1766+4203G>A		intron	N/A	NP_116114.1
	BUD13	NM_001159736.2		c.1364+4203G>A		intron	N/A	NP_001153208.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BUD13	ENST00000260210.5	TSL:1 MANE Select	c.1766+4203G>A		intron	N/A	ENSP00000260210.3
	BUD13	ENST00000375445.7	TSL:1	c.1364+4203G>A		intron	N/A	ENSP00000364594.3
	BUD13	ENST00000419189.1	TSL:5	n.*186+4203G>A		intron	N/A	ENSP00000415748.1

Frequencies

GnomAD3 genomes AF: 0.579 AC: 87969 AN: 151874 Hom.: 25876 Cov.: 31

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.583

Gnomad EAS AF: 0.636

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.627

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.579 AC: 87995 AN: 151992 Hom.: 25872 Cov.: 31 AF XY: 0.576 AC XY: 42755 AN XY: 74256

African (AFR) AF: 0.500 AC: 20744 AN: 41448

American (AMR) AF: 0.550 AC: 8389 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.583 AC: 2022 AN: 3470

East Asian (EAS) AF: 0.634 AC: 3285 AN: 5180

South Asian (SAS) AF: 0.598 AC: 2878 AN: 4810

European-Finnish (FIN) AF: 0.595 AC: 6264 AN: 10524

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.627 AC: 42616 AN: 67984

Other (OTH) AF: 0.557 AC: 1177 AN: 2112

Alfa AF: 0.603 Hom.: 14065

Bravo AF: 0.573

Asia WGS AF: 0.592 AC: 2061 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.028
DANN	Benign	0.52
PhyloP100		-1.9
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs180327; hg19: chr11-116623659;