rs10790162

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_032725.4(BUD13):​c.237+1741T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.929 in 152,252 control chromosomes in the GnomAD database, including 65,953 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 0.93 ( 65953 hom., cov: 32)

Consequence

BUD13
NM_032725.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.167
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
BUD13NM_032725.4 linkuse as main transcriptc.237+1741T>C intron_variant ENST00000260210.5
BUD13NM_001159736.2 linkuse as main transcriptc.237+1741T>C intron_variant
BUD13XM_011543035.3 linkuse as main transcriptc.138+1741T>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
BUD13ENST00000260210.5 linkuse as main transcriptc.237+1741T>C intron_variant 1 NM_032725.4 P2Q9BRD0-1
BUD13ENST00000375445.7 linkuse as main transcriptc.237+1741T>C intron_variant 1 A2Q9BRD0-2

Frequencies

GnomAD3 genomes
AF:
0.929
AC:
141338
AN:
152134
Hom.:
65902
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.984
Gnomad AMI
AF:
0.897
Gnomad AMR
AF:
0.886
Gnomad ASJ
AF:
0.910
Gnomad EAS
AF:
0.773
Gnomad SAS
AF:
0.810
Gnomad FIN
AF:
0.918
Gnomad MID
AF:
0.889
Gnomad NFE
AF:
0.929
Gnomad OTH
AF:
0.919
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.929
AC:
141445
AN:
152252
Hom.:
65953
Cov.:
32
AF XY:
0.925
AC XY:
68896
AN XY:
74446
show subpopulations
Gnomad4 AFR
AF:
0.984
Gnomad4 AMR
AF:
0.886
Gnomad4 ASJ
AF:
0.910
Gnomad4 EAS
AF:
0.772
Gnomad4 SAS
AF:
0.809
Gnomad4 FIN
AF:
0.918
Gnomad4 NFE
AF:
0.929
Gnomad4 OTH
AF:
0.914
Alfa
AF:
0.920
Hom.:
74415
Bravo
AF:
0.929
Asia WGS
AF:
0.804
AC:
2782
AN:
3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
3.2
DANN
Benign
0.73

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10790162; hg19: chr11-116639104; API