1-161152992-G-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PVS1_ModerateBP6_ModerateBS1BS2

The ENST00000467540.5(UFC1):​n.216+1G>C variant causes a splice donor, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00315 in 150,088 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0032 ( 5 hom., cov: 28)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

UFC1
ENST00000467540.5 splice_donor, intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.289
Variant links:
Genes affected
UFC1 (HGNC:26941): (ubiquitin-fold modifier conjugating enzyme 1) UFC1 is an E2-like conjugating enzyme for ubiquitin-fold modifier-1 (UFM1; MIM 610553) (Komatsu et al., 2004 [PubMed 15071506]).[supplied by OMIM, Mar 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

PVS1
Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene.
BP6
Variant 1-161152992-G-C is Benign according to our data. Variant chr1-161152992-G-C is described in ClinVar as [Benign]. Clinvar id is 3026802.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00315 (473/150088) while in subpopulation SAS AF= 0.0198 (94/4754). AF 95% confidence interval is 0.0165. There are 5 homozygotes in gnomad4. There are 260 alleles in male gnomad4 subpopulation. Median coverage is 28. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 5 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
UFC1ENST00000467540.5 linkuse as main transcriptn.216+1G>C splice_donor_variant, intron_variant 5

Frequencies

GnomAD3 genomes
AF:
0.00316
AC:
474
AN:
149970
Hom.:
5
Cov.:
28
show subpopulations
Gnomad AFR
AF:
0.000685
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00420
Gnomad ASJ
AF:
0.0153
Gnomad EAS
AF:
0.000200
Gnomad SAS
AF:
0.0198
Gnomad FIN
AF:
0.000100
Gnomad MID
AF:
0.00949
Gnomad NFE
AF:
0.00331
Gnomad OTH
AF:
0.00341
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
68
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
50
Gnomad4 AFR exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.00315
AC:
473
AN:
150088
Hom.:
5
Cov.:
28
AF XY:
0.00355
AC XY:
260
AN XY:
73164
show subpopulations
Gnomad4 AFR
AF:
0.000683
Gnomad4 AMR
AF:
0.00419
Gnomad4 ASJ
AF:
0.0153
Gnomad4 EAS
AF:
0.000201
Gnomad4 SAS
AF:
0.0198
Gnomad4 FIN
AF:
0.000100
Gnomad4 NFE
AF:
0.00331
Gnomad4 OTH
AF:
0.00290
Alfa
AF:
0.00344
Hom.:
0
Bravo
AF:
0.00282
Asia WGS
AF:
0.00751
AC:
26
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenFeb 01, 2024UFC1: BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
0.64
DANN
Benign
0.59

Splicing

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: rs181482336; hg19: chr1-161122782; API