rs17119975

chr11-116763841-T-C

Variant summary

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

The NM_032725.4(BUD13):c.323-575A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 152,244 control chromosomes in the GnomAD database, including 1,582 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 0.13 (1582 hom., cov: 32)
• Consequence: BUD13 NM_032725.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.453

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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BUD13	NM_032725.4	c.323-575A>G		intron_variant		ENST00000260210.5
BUD13	NM_001159736.2	c.323-575A>G		intron_variant
BUD13	XM_011543035.3	c.224-575A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BUD13	ENST00000260210.5	c.323-575A>G		intron_variant		1	NM_032725.4	P2
BUD13	ENST00000375445.7	c.323-575A>G		intron_variant		1		A2

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19185 AN: 152126 Hom.: 1582 Cov.: 32

Gnomad AFR AF: 0.0482

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.126 AC: 19193 AN: 152244 Hom.: 1582 Cov.: 32 AF XY: 0.132 AC XY: 9846 AN XY: 74436

Gnomad4 AFR AF: 0.0481

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.216

Gnomad4 SAS AF: 0.288

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.143

Gnomad4 OTH AF: 0.106

Alfa AF: 0.138 Hom.: 368

Bravo AF: 0.116

Asia WGS AF: 0.231 AC: 804 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	5.3
Dann	Benign	0.61

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: rs17119975; hg19: chr11-116634557;