rs17440396

Variant names:

• chr11-116751054-G-A
• rs17440396
• NM_032725.4:c.1767-2479C>T

Variant summary

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

The NM_032725.4(BUD13):​c.1767-2479C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0499 in 152,158 control chromosomes in the GnomAD database, including 267 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 0.050 (267 hom., cov: 32)
• Consequence: BUD13 NM_032725.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.530
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0971 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BUD13	NM_032725.4	c.1767-2479C>T		intron_variant	Intron 9 of 9	ENST00000260210.5	NP_116114.1
BUD13	NM_001159736.2	c.1365-2479C>T		intron_variant	Intron 9 of 9		NP_001153208.1
BUD13	XM_011543035.3	c.1668-2479C>T		intron_variant	Intron 9 of 9		XP_011541337.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BUD13	ENST00000260210.5	c.1767-2479C>T		intron_variant	Intron 9 of 9	1	NM_032725.4	ENSP00000260210.3
BUD13	ENST00000375445.7	c.1365-2479C>T		intron_variant	Intron 9 of 9	1		ENSP00000364594.3
BUD13	ENST00000419189.1	n.*187-2479C>T		intron_variant	Intron 3 of 3	5		ENSP00000415748.1
ENSG00000308823	ENST00000836679.1	n.433+12540G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0500 AC: 7606 AN: 152040 Hom.: 267 Cov.: 32

Gnomad AFR AF: 0.0142

Gnomad AMI AF: 0.0943

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.0478

Gnomad EAS AF: 0.0686

Gnomad SAS AF: 0.0472

Gnomad FIN AF: 0.0586

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0569

Gnomad OTH AF: 0.0589

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

GnomAD4 genome AF: 0.0499 AC: 7599 AN: 152158 Hom.: 267 Cov.: 32 AF XY: 0.0514 AC XY: 3822 AN XY: 74380

African (AFR) AF: 0.0142 AC: 588 AN: 41514

American (AMR) AF: 0.101 AC: 1550 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0478 AC: 166 AN: 3470

East Asian (EAS) AF: 0.0684 AC: 354 AN: 5174

South Asian (SAS) AF: 0.0471 AC: 227 AN: 4824

European-Finnish (FIN) AF: 0.0586 AC: 619 AN: 10562

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0569 AC: 3866 AN: 68002

Other (OTH) AF: 0.0573 AC: 121 AN: 2110

Alfa AF: 0.0612 Hom.: 58

Bravo AF: 0.0532

Asia WGS AF: 0.0680 AC: 235 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	1.6
DANN	Benign	0.46
PhyloP100		-0.53
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: rs17440396; hg19: chr11-116621770;