ENST00000482067.3:c.*105T>A
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong
The ENST00000482067.3(UMAD1):c.*105T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. 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 0.0 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
UMAD1
ENST00000482067.3 3_prime_UTR
ENST00000482067.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.825
Publications
54 publications found
Genes affected
UMAD1 (HGNC:48955): (UBAP1-MVB12-associated (UMA) domain containing 1)
GLCCI1-DT (HGNC:40852): (GLCCI1 divergent transcript)
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| GLCCI1-DT | NR_110018.1 | n.209+666A>T | intron_variant | Intron 1 of 4 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| UMAD1 | ENST00000482067.3 | c.*105T>A | 3_prime_UTR_variant | Exon 4 of 4 | 5 | ENSP00000490046.1 | ||||
| GLCCI1-DT | ENST00000428660.1 | n.132+1894A>T | intron_variant | Intron 1 of 1 | 4 | |||||
| GLCCI1-DT | ENST00000451066.2 | n.56+666A>T | intron_variant | Intron 1 of 3 | 5 |
Frequencies
GnomAD3 genomes 0.00 AC: 0AN: 152034Hom.: 0 Cov.: 32
GnomAD3 genomes
AF:
AC:
0
AN:
152034
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 244938Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 124098
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
244938
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
124098
African (AFR)
AF:
AC:
0
AN:
7152
American (AMR)
AF:
AC:
0
AN:
7404
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
9208
East Asian (EAS)
AF:
AC:
0
AN:
22810
South Asian (SAS)
AF:
AC:
0
AN:
2636
European-Finnish (FIN)
AF:
AC:
0
AN:
20670
Middle Eastern (MID)
AF:
AC:
0
AN:
1294
European-Non Finnish (NFE)
AF:
AC:
0
AN:
157472
Other (OTH)
AF:
AC:
0
AN:
16292
GnomAD4 genome 0.00 AC: 0AN: 152034Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74254
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
152034
Hom.:
Cov.:
32
AF XY:
AC XY:
0
AN XY:
74254
African (AFR)
AF:
AC:
0
AN:
41382
American (AMR)
AF:
AC:
0
AN:
15270
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3472
East Asian (EAS)
AF:
AC:
0
AN:
5186
South Asian (SAS)
AF:
AC:
0
AN:
4832
European-Finnish (FIN)
AF:
AC:
0
AN:
10574
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
0
AN:
68004
Other (OTH)
AF:
AC:
0
AN:
2088
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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