12-125517607-C-T

Variant summary

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

The NM_001366854.1(TMEM132B):​c.1107-1832C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.474 in 151,916 control chromosomes in the GnomAD database, including 20,767 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 0.47 ( 20767 hom., cov: 31)

Consequence

TMEM132B
NM_001366854.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.186

Publications

3 publications found
Variant links:
Genes affected
TMEM132B (HGNC:29397): (transmembrane protein 132B) Predicted to be integral component of membrane. [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=-1.02).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TMEM132BNM_001366854.1 linkc.1107-1832C>T intron_variant Intron 3 of 8 ENST00000682704.1 NP_001353783.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TMEM132BENST00000682704.1 linkc.1107-1832C>T intron_variant Intron 3 of 8 NM_001366854.1 ENSP00000507790.1 A0A804HK64
TMEM132BENST00000299308.7 linkc.1092-1832C>T intron_variant Intron 3 of 8 5 ENSP00000299308.3 Q14DG7-1
TMEM132BENST00000534945.2 linkn.1040-1832C>T intron_variant Intron 2 of 3 5

Frequencies

GnomAD3 genomes
AF:
0.473
AC:
71875
AN:
151800
Hom.:
20706
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.766
Gnomad AMI
AF:
0.228
Gnomad AMR
AF:
0.527
Gnomad ASJ
AF:
0.347
Gnomad EAS
AF:
0.850
Gnomad SAS
AF:
0.505
Gnomad FIN
AF:
0.346
Gnomad MID
AF:
0.354
Gnomad NFE
AF:
0.284
Gnomad OTH
AF:
0.428
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.474
AC:
72002
AN:
151916
Hom.:
20767
Cov.:
31
AF XY:
0.480
AC XY:
35628
AN XY:
74186
show subpopulations
African (AFR)
AF:
0.766
AC:
31795
AN:
41490
American (AMR)
AF:
0.528
AC:
8061
AN:
15266
Ashkenazi Jewish (ASJ)
AF:
0.347
AC:
1202
AN:
3466
East Asian (EAS)
AF:
0.850
AC:
4395
AN:
5170
South Asian (SAS)
AF:
0.505
AC:
2428
AN:
4808
European-Finnish (FIN)
AF:
0.346
AC:
3624
AN:
10472
Middle Eastern (MID)
AF:
0.364
AC:
107
AN:
294
European-Non Finnish (NFE)
AF:
0.284
AC:
19276
AN:
67930
Other (OTH)
AF:
0.429
AC:
907
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.510
Heterozygous variant carriers
0
1564
3129
4693
6258
7822
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
606
1212
1818
2424
3030
<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:
0.368
Hom.:
28162
Bravo
AF:
0.502
Asia WGS
AF:
0.685
AC:
2377
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
3.1
DANN
Benign
0.44
PhyloP100
-0.19
Mutation Taster
=100/0
polymorphism (auto)

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: rs2615666; hg19: chr12-126002153; API