chr12-125340568-G-A

Variant names:

• chr12-125340568-G-A
• rs7134868
• NM_001366854.1:c.68-8884G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001366854.1(TMEM132B):​c.68-8884G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.716 in 151,960 control chromosomes in the GnomAD database, including 39,049 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 0.72 (39049 hom., cov: 31)
• Consequence: TMEM132B NM_001366854.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.28
• Publications: 1 publications found

Genes affected

TMEM132B (HGNC:29397): (transmembrane protein 132B) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.801 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMEM132B	NM_001366854.1	c.68-8884G>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
TMEM132B	ENST00000682704.1	c.68-8884G>A		intron_variant	Intron 1 of 8		NM_001366854.1	ENSP00000507790.1
TMEM132B	ENST00000299308.7	c.53-8884G>A		intron_variant	Intron 1 of 8	5		ENSP00000299308.3
TMEM132B	ENST00000535330.1	n.227-8884G>A		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.716 AC: 108728 AN: 151842 Hom.: 39003 Cov.: 31

Gnomad AFR AF: 0.703

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.754

Gnomad ASJ AF: 0.712

Gnomad EAS AF: 0.703

Gnomad SAS AF: 0.821

Gnomad FIN AF: 0.764

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.714

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.716 AC: 108829 AN: 151960 Hom.: 39049 Cov.: 31 AF XY: 0.723 AC XY: 53695 AN XY: 74272

African (AFR) AF: 0.703 AC: 29116 AN: 41422

American (AMR) AF: 0.754 AC: 11517 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.712 AC: 2470 AN: 3468

East Asian (EAS) AF: 0.703 AC: 3624 AN: 5154

South Asian (SAS) AF: 0.822 AC: 3963 AN: 4820

European-Finnish (FIN) AF: 0.764 AC: 8049 AN: 10540

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.703 AC: 47806 AN: 67966

Other (OTH) AF: 0.714 AC: 1507 AN: 2112

Alfa AF: 0.707 Hom.: 77729

Bravo AF: 0.711

Asia WGS AF: 0.770 AC: 2673 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0060
DANN	Benign	0.24
PhyloP100		-2.3
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs7134868; hg19: chr12-125825114;