rs918143

Variant names:

• chr11-116759884-C-T
• rs918143
• NM_032725.4:c.1255-705G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032725.4(BUD13):​c.1255-705G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 151,980 control chromosomes in the GnomAD database, including 12,961 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 0.41 (12961 hom., cov: 32)
• Consequence: BUD13 NM_032725.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.378
• Publications: 9 publications found

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]

BUD13 Gene-Disease associations (from GenCC):

• progeroid syndrome

  Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

ENSG00000308823 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032725.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BUD13	NM_032725.4	MANE Select	c.1255-705G>A		intron	N/A	NP_116114.1	Q9BRD0-1
	BUD13	NM_001159736.2		c.853-705G>A		intron	N/A	NP_001153208.1	Q9BRD0-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BUD13	ENST00000260210.5	TSL:1 MANE Select	c.1255-705G>A		intron	N/A	ENSP00000260210.3	Q9BRD0-1
	BUD13	ENST00000375445.7	TSL:1	c.853-705G>A		intron	N/A	ENSP00000364594.3	Q9BRD0-2
	BUD13	ENST00000911264.1		c.1252-705G>A		intron	N/A	ENSP00000581323.1

Frequencies

GnomAD3 genomes AF: 0.408 AC: 61919 AN: 151862 Hom.: 12967 Cov.: 32

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.407 AC: 61928 AN: 151980 Hom.: 12961 Cov.: 32 AF XY: 0.396 AC XY: 29431 AN XY: 74286

African (AFR) AF: 0.415 AC: 17182 AN: 41448

American (AMR) AF: 0.309 AC: 4723 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.422 AC: 1465 AN: 3468

East Asian (EAS) AF: 0.350 AC: 1806 AN: 5156

South Asian (SAS) AF: 0.276 AC: 1328 AN: 4814

European-Finnish (FIN) AF: 0.362 AC: 3825 AN: 10562

Middle Eastern (MID) AF: 0.353 AC: 103 AN: 292

European-Non Finnish (NFE) AF: 0.446 AC: 30300 AN: 67944

Other (OTH) AF: 0.395 AC: 833 AN: 2110

Alfa AF: 0.433 Hom.: 25772

Bravo AF: 0.407

Asia WGS AF: 0.291 AC: 1014 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.1
DANN	Benign	0.49
PhyloP100		-0.38
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs918143; hg19: chr11-116630600;