Variant chr12-128297477-C-T details in Genebe, Genetics Data Aggregator

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

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]

TMEM132C links:

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	Effect	MANE	Protein	UniProt
TMEM132C	NM_001136103.3 link	c.85+29990C>T	intron_variant	ENST00000435159.3	NP_001129575.2	Q8N3T6
TMEM132C	NM_001387058.1 link	c.25+29183C>T	intron_variant		NP_001373987.1
TMEM132C	XM_047429886.1 link	c.85+29990C>T	intron_variant		XP_047285842.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TMEM132C	ENST00000435159.3 link	c.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.:

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.:

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over