rs10488699

Positions:

• chr11-116761784-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.1036+769G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0973 in 152,196 control chromosomes in the GnomAD database, including 890 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 0.097 (890 hom., cov: 33)
• Consequence: BUD13 NM_032725.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BUD13	NM_032725.4	c.1036+769G>A		intron_variant		ENST00000260210.5
BUD13	NM_001159736.2	c.635-832G>A		intron_variant
BUD13	XM_011543035.3	c.937+769G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BUD13	ENST00000260210.5	c.1036+769G>A		intron_variant		1	NM_032725.4	P2
BUD13	ENST00000375445.7	c.635-832G>A		intron_variant		1		A2
BUD13	ENST00000419189.1	c.284+769G>A		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0971 AC: 14766 AN: 152078 Hom.: 886 Cov.: 33

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.0709

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0459

Gnomad FIN AF: 0.0603

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0675

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.0973 AC: 14802 AN: 152196 Hom.: 890 Cov.: 33 AF XY: 0.0965 AC XY: 7179 AN XY: 74422

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.0709

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0462

Gnomad4 FIN AF: 0.0603

Gnomad4 NFE AF: 0.0675

Gnomad4 OTH AF: 0.104

Alfa AF: 0.0908 Hom.: 180

Bravo AF: 0.105

Asia WGS AF: 0.0400 AC: 140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.0
DANN	Benign	0.81

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: rs10488699; hg19: chr11-116632500;