chr12-128297477-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001136103.3(TMEM132C):​c.85+29990C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0925 in 152,214 control chromosomes in the GnomAD database, including 787 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 0.093 ( 787 hom., cov: 33)

Consequence

TMEM132C
NM_001136103.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.669
Variant links:
Genes affected
TMEM132C (HGNC:25436): (transmembrane protein 132C) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TMEM132CNM_001136103.3 linkc.85+29990C>T intron_variant ENST00000435159.3 NP_001129575.2 Q8N3T6
TMEM132CNM_001387058.1 linkc.25+29183C>T intron_variant NP_001373987.1
TMEM132CXM_047429886.1 linkc.85+29990C>T intron_variant XP_047285842.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TMEM132CENST00000435159.3 linkc.85+29990C>T intron_variant 5 NM_001136103.3 ENSP00000410852.2 Q8N3T6

Frequencies

GnomAD3 genomes
AF:
0.0926
AC:
14081
AN:
152094
Hom.:
784
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0953
Gnomad AMI
AF:
0.101
Gnomad AMR
AF:
0.0877
Gnomad ASJ
AF:
0.0741
Gnomad EAS
AF:
0.198
Gnomad SAS
AF:
0.190
Gnomad FIN
AF:
0.0741
Gnomad MID
AF:
0.0949
Gnomad NFE
AF:
0.0806
Gnomad OTH
AF:
0.0994
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0925
AC:
14087
AN:
152214
Hom.:
787
Cov.:
33
AF XY:
0.0936
AC XY:
6967
AN XY:
74430
show subpopulations
Gnomad4 AFR
AF:
0.0950
Gnomad4 AMR
AF:
0.0874
Gnomad4 ASJ
AF:
0.0741
Gnomad4 EAS
AF:
0.198
Gnomad4 SAS
AF:
0.190
Gnomad4 FIN
AF:
0.0741
Gnomad4 NFE
AF:
0.0806
Gnomad4 OTH
AF:
0.104
Alfa
AF:
0.0807
Hom.:
1127
Bravo
AF:
0.0942
Asia WGS
AF:
0.224
AC:
779
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
1.1
DANN
Benign
0.83

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs11059635; hg19: chr12-128782022; API