rs11825181

Variant names:

• chr11-116755542-G-A
• rs11825181
• NM_032725.4:c.1766+1604C>T

Your query was ambiguous. Multiple possible variants found:

• chr11-116755542-G-A
• chr11-116755542-G-C

Variant summary

Our verdict is Benign. Variant got -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

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=-0.82).
• 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

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

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.127

Gnomad4 ASJ AF: 0.0741

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0483

Gnomad4 FIN AF: 0.0601

Gnomad4 NFE AF: 0.0682

Gnomad4 OTH AF: 0.106

Alfa AF: 0.0621 Hom.: 118

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

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: rs11825181; hg19: chr11-116626258;