rs1043607

chr12-125658800-G-Achr12-125658800-G-Cchr12-125658800-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001366854.1(TMEM132B):c.*4090G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 152,038 control chromosomes in the GnomAD database, including 7,899 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 0.31 (7899 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: TMEM132B NM_001366854.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM132B	NM_001366854.1	c.*4090G>A		3_prime_UTR_variant	9/9	ENST00000682704.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM132B	ENST00000682704.1	c.*4090G>A		3_prime_UTR_variant	9/9		NM_001366854.1	P2
TMEM132B	ENST00000613307.1	c.*4090G>A		3_prime_UTR_variant	5/5	1
TMEM132B	ENST00000299308.7	c.*4090G>A		3_prime_UTR_variant	9/9	5		A2

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47290 AN: 151918 Hom.: 7880 Cov.: 33

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.270

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.311 AC: 47351 AN: 152038 Hom.: 7899 Cov.: 33 AF XY: 0.321 AC XY: 23874 AN XY: 74318

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.389

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.346

Gnomad4 SAS AF: 0.331

Gnomad4 FIN AF: 0.380

Gnomad4 NFE AF: 0.245

Gnomad4 OTH AF: 0.272

Alfa AF: 0.257 Hom.: 4386

Bravo AF: 0.314

Asia WGS AF: 0.375 AC: 1301 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.3
Dann	Benign	0.19

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

Other links and lift over

dbSNP: rs1043607; hg19: chr12-126143346;