11-116753987-G-T

Variant names:

• chr11-116753987-G-T
• rs180326
• NM_032725.4:c.1766+3159C>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.1766+3159C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.573 in 152,136 control chromosomes in the GnomAD database, including 25,828 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 0.57 (25828 hom., cov: 33)
• Consequence: BUD13 NM_032725.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 29 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=-1.07).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.747 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.1766+3159C>A		intron	N/A	NP_116114.1	Q9BRD0-1
	BUD13	NM_001159736.2		c.1364+3159C>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.1766+3159C>A		intron	N/A	ENSP00000260210.3	Q9BRD0-1
	BUD13	ENST00000375445.7	TSL:1	c.1364+3159C>A		intron	N/A	ENSP00000364594.3	Q9BRD0-2
	BUD13	ENST00000911264.1		c.1763+3159C>A		intron	N/A	ENSP00000581323.1

Frequencies

GnomAD3 genomes AF: 0.573 AC: 87147 AN: 152018 Hom.: 25826 Cov.: 33

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.767

Gnomad SAS AF: 0.652

Gnomad FIN AF: 0.632

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.563

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

GnomAD4 genome AF: 0.573 AC: 87177 AN: 152136 Hom.: 25828 Cov.: 33 AF XY: 0.575 AC XY: 42796 AN XY: 74378

African (AFR) AF: 0.422 AC: 17488 AN: 41460

American (AMR) AF: 0.581 AC: 8884 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.586 AC: 2034 AN: 3472

East Asian (EAS) AF: 0.767 AC: 3962 AN: 5168

South Asian (SAS) AF: 0.651 AC: 3135 AN: 4816

European-Finnish (FIN) AF: 0.632 AC: 6700 AN: 10596

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.634 AC: 43158 AN: 68020

Other (OTH) AF: 0.560 AC: 1184 AN: 2114

Alfa AF: 0.602 Hom.: 59570

Bravo AF: 0.560

Asia WGS AF: 0.695 AC: 2416 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.016
DANN	Benign	0.27
PhyloP100		-1.4
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: rs180326; hg19: chr11-116624703;