chr11-118535120-G-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_032780.4(TMEM25):c.*540G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 1,016,926 control chromosomes in the GnomAD database, including 11,554 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 0.16 ( 2453 hom., cov: 32)
Exomes 𝑓: 0.14 ( 9101 hom. )
Consequence
TMEM25
NM_032780.4 3_prime_UTR
NM_032780.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.494
Publications
17 publications found
Genes affected
TMEM25 (HGNC:25890): (transmembrane protein 25) Predicted to be involved in negative regulation of excitatory postsynaptic potential and regulation of protein stability. Predicted to be located in late endosome and lysosome. [provided by Alliance of Genome Resources, Apr 2022]
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=-0.75).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.161 AC: 24505AN: 151918Hom.: 2456 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
24505
AN:
151918
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 AF: 0.138 AC: 119110AN: 864890Hom.: 9101 Cov.: 33 AF XY: 0.138 AC XY: 55471AN XY: 400698 show subpopulations
GnomAD4 exome
AF:
AC:
119110
AN:
864890
Hom.:
Cov.:
33
AF XY:
AC XY:
55471
AN XY:
400698
show subpopulations
African (AFR)
AF:
AC:
2911
AN:
16782
American (AMR)
AF:
AC:
237
AN:
3130
Ashkenazi Jewish (ASJ)
AF:
AC:
856
AN:
6126
East Asian (EAS)
AF:
AC:
2498
AN:
5166
South Asian (SAS)
AF:
AC:
5917
AN:
18014
European-Finnish (FIN)
AF:
AC:
306
AN:
2062
Middle Eastern (MID)
AF:
AC:
276
AN:
1720
European-Non Finnish (NFE)
AF:
AC:
101123
AN:
782714
Other (OTH)
AF:
AC:
4986
AN:
29176
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.483
Heterozygous variant carriers
0
7092
14184
21276
28368
35460
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
5114
10228
15342
20456
25570
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome AF: 0.161 AC: 24518AN: 152036Hom.: 2453 Cov.: 32 AF XY: 0.166 AC XY: 12308AN XY: 74334 show subpopulations
GnomAD4 genome
AF:
AC:
24518
AN:
152036
Hom.:
Cov.:
32
AF XY:
AC XY:
12308
AN XY:
74334
show subpopulations
African (AFR)
AF:
AC:
7224
AN:
41450
American (AMR)
AF:
AC:
1467
AN:
15278
Ashkenazi Jewish (ASJ)
AF:
AC:
513
AN:
3468
East Asian (EAS)
AF:
AC:
2532
AN:
5140
South Asian (SAS)
AF:
AC:
1629
AN:
4824
European-Finnish (FIN)
AF:
AC:
1727
AN:
10574
Middle Eastern (MID)
AF:
AC:
34
AN:
294
European-Non Finnish (NFE)
AF:
AC:
8923
AN:
67988
Other (OTH)
AF:
AC:
332
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.506
Heterozygous variant carriers
0
1033
2065
3098
4130
5163
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
282
564
846
1128
1410
<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:
1472
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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