rs1263149

chr11-116769225-A-Gchr11-116769225-A-T

Variant summary

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

The NM_032725.4(BUD13):c.237+904T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.507 in 151,674 control chromosomes in the GnomAD database, including 19,583 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 0.51 (19583 hom., cov: 30)
• Consequence: BUD13 NM_032725.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0900

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BUD13	NM_032725.4	c.237+904T>C		intron_variant		ENST00000260210.5
BUD13	NM_001159736.2	c.237+904T>C		intron_variant
BUD13	XM_011543035.3	c.138+904T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BUD13	ENST00000260210.5	c.237+904T>C		intron_variant		1	NM_032725.4	P2
BUD13	ENST00000375445.7	c.237+904T>C		intron_variant		1		A2

Frequencies

GnomAD3 genomes AF: 0.506 AC: 76757 AN: 151556 Hom.: 19555 Cov.: 30

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.505

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.562

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.510

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

GnomAD4 genome AF: 0.507 AC: 76846 AN: 151674 Hom.: 19583 Cov.: 30 AF XY: 0.515 AC XY: 38126 AN XY: 74076

Gnomad4 AFR AF: 0.501

Gnomad4 AMR AF: 0.568

Gnomad4 ASJ AF: 0.493

Gnomad4 EAS AF: 0.425

Gnomad4 SAS AF: 0.533

Gnomad4 FIN AF: 0.562

Gnomad4 NFE AF: 0.492

Gnomad4 OTH AF: 0.510

Alfa AF: 0.499 Hom.: 9219

Bravo AF: 0.504

Asia WGS AF: 0.511 AC: 1776 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.6
Dann	Benign	0.47

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: rs1263149; hg19: chr11-116639941;