Genetic Variant TMEM132B:c.68-23040T>C (chr12-125326412-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001366854.1(TMEM132B):c.68-23040T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.643 in 605,446 control chromosomes in the GnomAD database, including 128,240 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 0.67 ( 35301 hom., cov: 31)

Exomes 𝑓: 0.63 ( 92939 hom. )

Consequence

TMEM132B
NM_001366854.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.50

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]

TMEM132B links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMEM132B	NM_001366854.1 link	c.68-23040T>C		intron_variant	Intron 1 of 8	ENST00000682704.1	NP_001353783.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
TMEM132B	ENST00000682704.1 link	c.68-23040T>C	intron_variant	Intron 1 of 8		NM_001366854.1	ENSP00000507790.1	A0A804HK64
TMEM132B	ENST00000299308.7 link	c.-212T>C	upstream_gene_variant		5		ENSP00000299308.3	Q14DG7-1
TMEM132B	ENST00000535330.1 link	n.-139T>C	upstream_gene_variant		4

Frequencies

GnomAD3 genomes

AF:

0.674

AC:

102374

AN:

151902

Hom.:

35251

Cov.:

show subpopulations

Gnomad AFR

AF:

0.794

Gnomad AMI

AF:

0.595

Gnomad AMR

AF:

0.719

Gnomad ASJ

AF:

0.644

Gnomad EAS

AF:

0.812

Gnomad SAS

AF:

0.764

Gnomad FIN

AF:

0.665

Gnomad MID

AF:

0.639

Gnomad NFE

AF:

0.578

Gnomad OTH

AF:

0.672

GnomAD4 exome

AF:

0.632

AC:

286625

AN:

453426

Hom.:

92939

AF XY:

0.637

AC XY:

152950

AN XY:

240058

show subpopulations

Gnomad4 AFR exome

AF:

0.796

Gnomad4 AMR exome

AF:

0.742

Gnomad4 ASJ exome

AF:

0.647

Gnomad4 EAS exome

AF:

0.818

Gnomad4 SAS exome

AF:

0.745

Gnomad4 FIN exome

AF:

0.632

Gnomad4 NFE exome

AF:

0.574

Gnomad4 OTH exome

AF:

0.629

GnomAD4 genome

AF:

0.674

AC:

102481

AN:

152020

Hom.:

35301

Cov.:

AF XY:

0.685

AC XY:

50911

AN XY:

74322

show subpopulations

Gnomad4 AFR

AF:

0.794

Gnomad4 AMR

AF:

0.720

Gnomad4 ASJ

AF:

0.644

Gnomad4 EAS

AF:

0.812

Gnomad4 SAS

AF:

0.762

Gnomad4 FIN

AF:

0.665

Gnomad4 NFE

AF:

0.578

Gnomad4 OTH

AF:

0.675

Alfa

AF:

0.606

Hom.:

36454

Bravo

AF:

0.684

Asia WGS

AF:

0.818

AC:

2843

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

DANN

Benign

0.67

Splicing

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