chr11-116755542-G-A

Variant names:

• chr11-116755542-G-A
• rs11825181
• NM_032725.4:c.1766+1604C>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.1766+1604C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,226 control chromosomes in the GnomAD database, including 995 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 0.10 (995 hom., cov: 33)
• Consequence: BUD13 NM_032725.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.488
• Publications: 30 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BUD13	NM_032725.4	c.1766+1604C>T		intron_variant	Intron 9 of 9	ENST00000260210.5	NP_116114.1
BUD13	NM_001159736.2	c.1364+1604C>T		intron_variant	Intron 9 of 9		NP_001153208.1
BUD13	XM_011543035.3	c.1667+1604C>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.1766+1604C>T		intron_variant	Intron 9 of 9	1	NM_032725.4	ENSP00000260210.3
BUD13	ENST00000375445.7	c.1364+1604C>T		intron_variant	Intron 9 of 9	1		ENSP00000364594.3
BUD13	ENST00000419189.1	n.*186+1604C>T		intron_variant	Intron 3 of 3	5		ENSP00000415748.1
ENSG00000308823	ENST00000836679.1	n.434-9708G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15358 AN: 152108 Hom.: 990 Cov.: 33

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.0741

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0480

Gnomad FIN AF: 0.0601

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0682

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.101 AC: 15392 AN: 152226 Hom.: 995 Cov.: 33 AF XY: 0.100 AC XY: 7457 AN XY: 74436

African (AFR) AF: 0.176 AC: 7304 AN: 41528

American (AMR) AF: 0.127 AC: 1949 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0741 AC: 257 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5190

South Asian (SAS) AF: 0.0483 AC: 233 AN: 4828

European-Finnish (FIN) AF: 0.0601 AC: 638 AN: 10614

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0682 AC: 4637 AN: 67988

Other (OTH) AF: 0.106 AC: 224 AN: 2108

Alfa AF: 0.0749 Hom.: 886

Bravo AF: 0.109

Asia WGS AF: 0.0410 AC: 143 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.0
DANN	Benign	0.78
PhyloP100		-0.49
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: rs11825181; hg19: chr11-116626258;