NM_001366854.1:c.*4090G>A

Variant names:

• chr12-125658800-G-A
• rs1043607
• NM_001366854.1:c.*4090G>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.*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
• Publications: 6 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001366854.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM132B	NM_001366854.1	MANE Select	c.*4090G>A		3_prime_UTR	Exon 9 of 9	NP_001353783.1
	TMEM132B	NM_052907.3		c.*4090G>A		3_prime_UTR	Exon 9 of 9	NP_443139.2
	TMEM132B	NM_001286219.2		c.*4090G>A		3_prime_UTR	Exon 5 of 5	NP_001273148.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM132B	ENST00000682704.1	MANE Select	c.*4090G>A		3_prime_UTR	Exon 9 of 9	ENSP00000507790.1
	TMEM132B	ENST00000613307.1	TSL:1	c.*4090G>A		3_prime_UTR	Exon 5 of 5	ENSP00000482788.1
	TMEM132B	ENST00000299308.7	TSL:5	c.*4090G>A		3_prime_UTR	Exon 9 of 9	ENSP00000299308.3

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.391 AC: 16219 AN: 41448

American (AMR) AF: 0.389 AC: 5944 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 431 AN: 3470

East Asian (EAS) AF: 0.346 AC: 1792 AN: 5176

South Asian (SAS) AF: 0.331 AC: 1596 AN: 4824

European-Finnish (FIN) AF: 0.380 AC: 4008 AN: 10552

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.245 AC: 16637 AN: 67968

Other (OTH) AF: 0.272 AC: 575 AN: 2112

Alfa AF: 0.259 Hom.: 5145

Bravo AF: 0.314

Asia WGS AF: 0.375 AC: 1301 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.19
PhyloP100		-0.83
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: rs1043607; hg19: chr12-126143346;