11-116753437-C-G

Position:

• chr11-116753437-C-G

Variant summary

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

The NM_032725.4(BUD13):​c.1766+3709G>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 152,310 control chromosomes in the GnomAD database, including 65,996 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 (65996 hom., cov: 33)
• Consequence: BUD13 NM_032725.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15

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=-0.92).
• 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	Protein	UniProt
BUD13	NM_032725.4	c.1766+3709G>C		intron_variant		ENST00000260210.5	NP_116114.1
BUD13	NM_001159736.2	c.1364+3709G>C		intron_variant			NP_001153208.1
BUD13	XM_011543035.3	c.1667+3709G>C		intron_variant			XP_011541337.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BUD13	ENST00000260210.5	c.1766+3709G>C		intron_variant		1	NM_032725.4	ENSP00000260210.3
BUD13	ENST00000375445.7	c.1364+3709G>C		intron_variant		1		ENSP00000364594.3
BUD13	ENST00000419189.1	n.*186+3709G>C		intron_variant		5		ENSP00000415748.1

Frequencies

GnomAD3 genomes AF: 0.929 AC: 141410 AN: 152192 Hom.: 65943 Cov.: 33

Gnomad AFR AF: 0.984

Gnomad AMI AF: 0.897

Gnomad AMR AF: 0.886

Gnomad ASJ AF: 0.911

Gnomad EAS AF: 0.771

Gnomad SAS AF: 0.806

Gnomad FIN AF: 0.919

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.930

Gnomad OTH AF: 0.922

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

GnomAD4 genome AF: 0.929 AC: 141519 AN: 152310 Hom.: 65996 Cov.: 33 AF XY: 0.925 AC XY: 68912 AN XY: 74466

Gnomad4 AFR AF: 0.984

Gnomad4 AMR AF: 0.886

Gnomad4 ASJ AF: 0.911

Gnomad4 EAS AF: 0.770

Gnomad4 SAS AF: 0.806

Gnomad4 FIN AF: 0.919

Gnomad4 NFE AF: 0.930

Gnomad4 OTH AF: 0.917

Alfa AF: 0.917 Hom.: 3011

Bravo AF: 0.929

Asia WGS AF: 0.803 AC: 2795 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.32
DANN	Benign	0.54

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: rs6589564; hg19: chr11-116624153;