GeneBe

NM_001366854.1:c.68-23040T>A

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001366854.1(TMEM132B):​c.68-23040T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

TMEM132B
NM_001366854.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.50

Publications

8 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]

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TMEM132BNM_001366854.1 linkc.68-23040T>A intron_variant Intron 1 of 8 ENST00000682704.1 NP_001353783.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TMEM132BENST00000682704.1 linkc.68-23040T>A intron_variant Intron 1 of 8 NM_001366854.1 ENSP00000507790.1 A0A804HK64
TMEM132BENST00000299308.7 linkc.-212T>A upstream_gene_variant 5 ENSP00000299308.3 Q14DG7-1
TMEM132BENST00000535330.1 linkn.-139T>A upstream_gene_variant 4

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
0.00
AC:
0
AN:
454222
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
240460
African (AFR)
AF:
0.00
AC:
0
AN:
12878
American (AMR)
AF:
0.00
AC:
0
AN:
24588
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
14448
East Asian (EAS)
AF:
0.00
AC:
0
AN:
28722
South Asian (SAS)
AF:
0.00
AC:
0
AN:
48636
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
27790
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
2114
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
269340
Other (OTH)
AF:
0.00
AC:
0
AN:
25706
GnomAD4 genome
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.79
CADD
Benign
14
DANN
Benign
0.80
PhyloP100
1.5
PromoterAI
0.0015
Neutral

Splicing

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

Publications

Other links and lift over

dbSNP: rs551601; hg19: chr12-125810958; API