rs180327

chr11-116752943-C-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BUD13	NM_032725.4	c.1766+4203G>A		intron_variant		ENST00000260210.5
BUD13	NM_001159736.2	c.1364+4203G>A		intron_variant
BUD13	XM_011543035.3	c.1667+4203G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BUD13	ENST00000260210.5	c.1766+4203G>A		intron_variant		1	NM_032725.4	P2
BUD13	ENST00000375445.7	c.1364+4203G>A		intron_variant		1		A2
BUD13	ENST00000419189.1	c.*186+4203G>A		intron_variant, NMD_transcript_variant		5

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

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.550

Gnomad4 ASJ AF: 0.583

Gnomad4 EAS AF: 0.634

Gnomad4 SAS AF: 0.598

Gnomad4 FIN AF: 0.595

Gnomad4 NFE AF: 0.627

Gnomad4 OTH AF: 0.557

Alfa AF: 0.603 Hom.: 8560

Bravo AF: 0.573

Asia WGS AF: 0.592 AC: 2061 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.028
Dann	Benign	0.52

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: rs180327; hg19: chr11-116623659;