GeneBe

rs1191267919

Variant names:

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_001252275.3(UGT2A1):​c.716-7delT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.31 ( 2843 hom., cov: 0)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

UGT2A1
NM_001252275.3 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.249

Publications

0 publications found
Variant links:
Genes affected
UGT2A2 (HGNC:28183): (UDP glucuronosyltransferase family 2 member A2) The protein encoded by this gene belongs to the UDP-glycosyltransferase family. Members of this protein family play a role in the conjugation and subsequent elimination of potentially toxic xenobiotics and endogenous compounds. The encoded enzyme is expressed in the olfactory neuroepithelium, which lines the posterior nasal cavity and is exposed to a wide range of odorants and airborne toxic compounds. Hence, this protein has been suggested to be involved in clearing lipophilic odorant molecules from the sensory epithelium. This gene shares exon structure with the UDP glucuronosyltransferase 2A1 family member, which encodes N-terminally distinct isoforms. Polymorphisms in this gene may be associated with the loss of taste and smell that is reported by some individuals during SARS-CoV-2 infection. [provided by RefSeq, Jan 2022]
UGT2A1 (HGNC:12542): (UDP glucuronosyltransferase family 2 member A1 complex locus) The protein encoded by this gene belongs to the UDP-glycosyltransferase family. Members of this protein family play a role in the conjugation and subsequent elimination of potentially toxic xenobiotics and endogenous compounds. The encoded enzyme is expressed in the olfactory neuroepithelium, which lines the posterior nasal cavity and is exposed to a wide range of odorants and airborne toxic compounds. Hence, this protein has been suggested to be involved in clearing lipophilic odorant molecules from the sensory epithelium. This gene shares exon structure with the UDP glucuronosyltransferase 2A2 family member, which encodes N-terminally distinct isoforms. Polymorphisms in this gene may be associated with the loss of taste and smell that is reported by some individuals during SARS-CoV-2 infection. [provided by RefSeq, Jan 2022]

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001252275.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
UGT2A2
NM_001105677.2
MANE Select
c.742+3070delT
intron
N/ANP_001099147.2P0DTE5-1
UGT2A1
NM_001252275.3
MANE Select
c.716-7delT
splice_region intron
N/ANP_001239204.2P0DTE4-5
UGT2A1
NM_001389565.1
c.1345+3070delT
intron
N/ANP_001376494.1

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
UGT2A2
ENST00000604629.6
TSL:1 MANE Select
c.742+3070delT
intron
N/AENSP00000475028.2P0DTE5-1
UGT2A1
ENST00000286604.9
TSL:1 MANE Select
c.716-7delT
splice_region intron
N/AENSP00000286604.4P0DTE4-5
UGT2A1
ENST00000503640.5
TSL:1
c.715+11101delT
intron
N/AENSP00000424478.1P0DTE4-1

Frequencies

GnomAD3 genomes
AF:
0.306
AC:
14683
AN:
48020
Hom.:
2842
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.148
Gnomad AMI
AF:
0.264
Gnomad AMR
AF:
0.319
Gnomad ASJ
AF:
0.377
Gnomad EAS
AF:
0.287
Gnomad SAS
AF:
0.340
Gnomad FIN
AF:
0.689
Gnomad MID
AF:
0.500
Gnomad NFE
AF:
0.381
Gnomad OTH
AF:
0.341
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
0.00
AC:
0
AN:
2
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
2
African (AFR)
AC:
0
AN:
0
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AF:
0.00
AC:
0
AN:
2
European-Finnish (FIN)
AC:
0
AN:
0
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AC:
0
AN:
0
Other (OTH)
AC:
0
AN:
0
GnomAD4 genome
AF:
0.306
AC:
14685
AN:
48026
Hom.:
2843
Cov.:
0
AF XY:
0.311
AC XY:
6622
AN XY:
21300
show subpopulations
African (AFR)
AF:
0.148
AC:
2195
AN:
14826
American (AMR)
AF:
0.319
AC:
977
AN:
3062
Ashkenazi Jewish (ASJ)
AF:
0.377
AC:
485
AN:
1286
East Asian (EAS)
AF:
0.287
AC:
412
AN:
1434
South Asian (SAS)
AF:
0.343
AC:
268
AN:
782
European-Finnish (FIN)
AF:
0.689
AC:
598
AN:
868
Middle Eastern (MID)
AF:
0.500
AC:
22
AN:
44
European-Non Finnish (NFE)
AF:
0.381
AC:
9442
AN:
24808
Other (OTH)
AF:
0.342
AC:
194
AN:
568
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.441
Heterozygous variant carriers
0
305
611
916
1222
1527
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
140
280
420
560
700
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.00
Hom.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.25
Mutation Taster
=100/0
polymorphism

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

Other links and lift over

dbSNP: rs1191267919; hg19: chr4-70501546; API