11-116769521-A-G

Position:

• chr11-116769521-A-G

Variant summary

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

The NM_032725.4(BUD13):​c.237+608T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.929 in 152,280 control chromosomes in the GnomAD database, including 65,963 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 0.93 (65963 hom., cov: 32)
• Consequence: BUD13 NM_032725.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0800

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BUD13	NM_032725.4	c.237+608T>C		intron_variant		ENST00000260210.5
BUD13	NM_001159736.2	c.237+608T>C		intron_variant
BUD13	XM_011543035.3	c.138+608T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BUD13	ENST00000260210.5	c.237+608T>C		intron_variant		1	NM_032725.4	P2
BUD13	ENST00000375445.7	c.237+608T>C		intron_variant		1		A2

Frequencies

GnomAD3 genomes AF: 0.929 AC: 141360 AN: 152162 Hom.: 65912 Cov.: 32

Gnomad AFR AF: 0.984

Gnomad AMI AF: 0.897

Gnomad AMR AF: 0.886

Gnomad ASJ AF: 0.910

Gnomad EAS AF: 0.772

Gnomad SAS AF: 0.809

Gnomad FIN AF: 0.918

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.929

Gnomad OTH AF: 0.919

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

GnomAD4 genome AF: 0.929 AC: 141467 AN: 152280 Hom.: 65963 Cov.: 32 AF XY: 0.925 AC XY: 68913 AN XY: 74464

Gnomad4 AFR AF: 0.984

Gnomad4 AMR AF: 0.886

Gnomad4 ASJ AF: 0.910

Gnomad4 EAS AF: 0.771

Gnomad4 SAS AF: 0.808

Gnomad4 FIN AF: 0.918

Gnomad4 NFE AF: 0.929

Gnomad4 OTH AF: 0.914

Alfa AF: 0.938 Hom.: 9833

Bravo AF: 0.929

Asia WGS AF: 0.805 AC: 2803 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.2
DANN	Benign	0.59

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: rs6589565; hg19: chr11-116640237;