rs7134868

Positions:

• chr12-125340568-G-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
TMEM132B	NM_001366854.1	c.68-8884G>A		intron_variant		ENST00000682704.1	NP_001353783.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TMEM132B	ENST00000682704.1	c.68-8884G>A		intron_variant			NM_001366854.1	ENSP00000507790	P2
TMEM132B	ENST00000299308.7	c.53-8884G>A		intron_variant		5		ENSP00000299308	A2
TMEM132B	ENST00000535330.1	n.227-8884G>A		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.703

Gnomad4 AMR AF: 0.754

Gnomad4 ASJ AF: 0.712

Gnomad4 EAS AF: 0.703

Gnomad4 SAS AF: 0.822

Gnomad4 FIN AF: 0.764

Gnomad4 NFE AF: 0.703

Gnomad4 OTH AF: 0.714

Alfa AF: 0.706 Hom.: 19320

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs7134868; hg19: chr12-125825114;