12-125517607-C-T

Variant names:

• chr12-125517607-C-T
• rs2615666
• NM_001366854.1:c.1107-1832C>T

Variant summary

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

The NM_001366854.1(TMEM132B):​c.1107-1832C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.474 in 151,916 control chromosomes in the GnomAD database, including 20,767 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 0.47 (20767 hom., cov: 31)
• Consequence: TMEM132B NM_001366854.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.186
• Publications: 3 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMEM132B	NM_001366854.1	c.1107-1832C>T		intron_variant	Intron 3 of 8	ENST00000682704.1	NP_001353783.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM132B	ENST00000682704.1	c.1107-1832C>T		intron_variant	Intron 3 of 8		NM_001366854.1	ENSP00000507790.1
TMEM132B	ENST00000299308.7	c.1092-1832C>T		intron_variant	Intron 3 of 8	5		ENSP00000299308.3
TMEM132B	ENST00000534945.2	n.1040-1832C>T		intron_variant	Intron 2 of 3	5

Frequencies

GnomAD3 genomes AF: 0.473 AC: 71875 AN: 151800 Hom.: 20706 Cov.: 31

Gnomad AFR AF: 0.766

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.850

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.474 AC: 72002 AN: 151916 Hom.: 20767 Cov.: 31 AF XY: 0.480 AC XY: 35628 AN XY: 74186

African (AFR) AF: 0.766 AC: 31795 AN: 41490

American (AMR) AF: 0.528 AC: 8061 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 1202 AN: 3466

East Asian (EAS) AF: 0.850 AC: 4395 AN: 5170

South Asian (SAS) AF: 0.505 AC: 2428 AN: 4808

European-Finnish (FIN) AF: 0.346 AC: 3624 AN: 10472

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.284 AC: 19276 AN: 67930

Other (OTH) AF: 0.429 AC: 907 AN: 2112

Alfa AF: 0.368 Hom.: 28162

Bravo AF: 0.502

Asia WGS AF: 0.685 AC: 2377 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.1
DANN	Benign	0.44
PhyloP100		-0.19
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2615666; hg19: chr12-126002153;