chr7-7825120-A-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001302348.2(UMAD1):​c.156+23377A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.792 in 151,984 control chromosomes in the GnomAD database, including 47,725 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 0.79 ( 47725 hom., cov: 30)

Consequence

UMAD1
NM_001302348.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.109

Publications

5 publications found
Variant links:
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=-0.97).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.83 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
UMAD1NM_001302348.2 linkc.156+23377A>G intron_variant Intron 3 of 3 ENST00000682710.1 NP_001289277.1 C9J7I0
UMAD1NM_001302349.2 linkc.156+23377A>G intron_variant Intron 3 of 3 NP_001289278.1 C9J7I0
UMAD1NM_001302350.2 linkc.51+23377A>G intron_variant Intron 4 of 4 NP_001289279.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
UMAD1ENST00000682710.1 linkc.156+23377A>G intron_variant Intron 3 of 3 NM_001302348.2 ENSP00000507605.1 C9J7I0

Frequencies

GnomAD3 genomes
AF:
0.792
AC:
120261
AN:
151866
Hom.:
47690
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.837
Gnomad AMI
AF:
0.795
Gnomad AMR
AF:
0.749
Gnomad ASJ
AF:
0.767
Gnomad EAS
AF:
0.761
Gnomad SAS
AF:
0.807
Gnomad FIN
AF:
0.815
Gnomad MID
AF:
0.777
Gnomad NFE
AF:
0.774
Gnomad OTH
AF:
0.766
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.792
AC:
120349
AN:
151984
Hom.:
47725
Cov.:
30
AF XY:
0.794
AC XY:
59001
AN XY:
74266
show subpopulations
African (AFR)
AF:
0.837
AC:
34715
AN:
41462
American (AMR)
AF:
0.749
AC:
11420
AN:
15242
Ashkenazi Jewish (ASJ)
AF:
0.767
AC:
2660
AN:
3470
East Asian (EAS)
AF:
0.761
AC:
3914
AN:
5144
South Asian (SAS)
AF:
0.808
AC:
3891
AN:
4816
European-Finnish (FIN)
AF:
0.815
AC:
8635
AN:
10596
Middle Eastern (MID)
AF:
0.764
AC:
223
AN:
292
European-Non Finnish (NFE)
AF:
0.774
AC:
52565
AN:
67946
Other (OTH)
AF:
0.761
AC:
1604
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.506
Heterozygous variant carriers
0
1269
2538
3808
5077
6346
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
872
1744
2616
3488
4360
<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:
0.776
Hom.:
197463
Bravo
AF:
0.787
Asia WGS
AF:
0.783
AC:
2728
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
3.9
DANN
Benign
0.72
PhyloP100
0.11
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs12702661; hg19: chr7-7864751; API