chr7-7734210-T-C
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001302348.2(UMAD1):c.82+60757T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,070 control chromosomes in the GnomAD database, including 1,357 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 0.13 ( 1357 hom., cov: 31)
Consequence
UMAD1
NM_001302348.2 intron
NM_001302348.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.320
Publications
6 publications found
Genes affected
UMAD1 (HGNC:48955): (UBAP1-MVB12-associated (UMA) domain containing 1)
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
UMAD1 | NM_001302348.2 | c.82+60757T>C | intron_variant | Intron 2 of 3 | ENST00000682710.1 | NP_001289277.1 | ||
UMAD1 | NM_001302349.2 | c.82+60757T>C | intron_variant | Intron 2 of 3 | NP_001289278.1 | |||
UMAD1 | NM_001302350.2 | c.-24+58002T>C | intron_variant | Intron 3 of 4 | NP_001289279.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.134 AC: 20362AN: 151950Hom.: 1354 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
20362
AN:
151950
Hom.:
Cov.:
31
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.134 AC: 20397AN: 152070Hom.: 1357 Cov.: 31 AF XY: 0.133 AC XY: 9854AN XY: 74370 show subpopulations
GnomAD4 genome
AF:
AC:
20397
AN:
152070
Hom.:
Cov.:
31
AF XY:
AC XY:
9854
AN XY:
74370
show subpopulations
African (AFR)
AF:
AC:
6418
AN:
41490
American (AMR)
AF:
AC:
1561
AN:
15276
Ashkenazi Jewish (ASJ)
AF:
AC:
538
AN:
3460
East Asian (EAS)
AF:
AC:
501
AN:
5188
South Asian (SAS)
AF:
AC:
767
AN:
4822
European-Finnish (FIN)
AF:
AC:
996
AN:
10572
Middle Eastern (MID)
AF:
AC:
61
AN:
294
European-Non Finnish (NFE)
AF:
AC:
8953
AN:
67946
Other (OTH)
AF:
AC:
329
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
897
1794
2691
3588
4485
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
230
460
690
920
1150
<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:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
567
AN:
3478
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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