11-116753987-G-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+3159C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.573 in 152,136 control chromosomes in the GnomAD database, including 25,828 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 (25828 hom., cov: 33)
• Consequence: BUD13 NM_032725.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40

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=-1.07).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BUD13	NM_032725.4	c.1766+3159C>A		intron_variant		ENST00000260210.5
BUD13	NM_001159736.2	c.1364+3159C>A		intron_variant
BUD13	XM_011543035.3	c.1667+3159C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BUD13	ENST00000260210.5	c.1766+3159C>A		intron_variant		1	NM_032725.4	P2
BUD13	ENST00000375445.7	c.1364+3159C>A		intron_variant		1		A2
BUD13	ENST00000419189.1	c.*186+3159C>A		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.573 AC: 87147 AN: 152018 Hom.: 25826 Cov.: 33

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.767

Gnomad SAS AF: 0.652

Gnomad FIN AF: 0.632

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.563

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

GnomAD4 genome AF: 0.573 AC: 87177 AN: 152136 Hom.: 25828 Cov.: 33 AF XY: 0.575 AC XY: 42796 AN XY: 74378

Gnomad4 AFR AF: 0.422

Gnomad4 AMR AF: 0.581

Gnomad4 ASJ AF: 0.586

Gnomad4 EAS AF: 0.767

Gnomad4 SAS AF: 0.651

Gnomad4 FIN AF: 0.632

Gnomad4 NFE AF: 0.634

Gnomad4 OTH AF: 0.560

Alfa AF: 0.620 Hom.: 40555

Bravo AF: 0.560

Asia WGS AF: 0.695 AC: 2416 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.016
Dann	Benign	0.27

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: rs180326; hg19: chr11-116624703;