rs11058197

Positions:

• chr12-125483798-G-A
• chr12-125483798-G-C

Variant summary

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

The NM_001366854.1(TMEM132B):​c.1107-35641G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 151,986 control chromosomes in the GnomAD database, including 8,006 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 0.32 (8006 hom., cov: 32)
• Consequence: TMEM132B NM_001366854.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0400

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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.499 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM132B	NM_001366854.1	c.1107-35641G>A		intron_variant		ENST00000682704.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM132B	ENST00000682704.1	c.1107-35641G>A		intron_variant			NM_001366854.1	P2
TMEM132B	ENST00000299308.7	c.1092-35641G>A		intron_variant		5		A2
TMEM132B	ENST00000534945.2	n.1040-35641G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48677 AN: 151868 Hom.: 8015 Cov.: 32

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.317

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.320 AC: 48691 AN: 151986 Hom.: 8006 Cov.: 32 AF XY: 0.321 AC XY: 23819 AN XY: 74272

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.337

Gnomad4 ASJ AF: 0.306

Gnomad4 EAS AF: 0.515

Gnomad4 SAS AF: 0.327

Gnomad4 FIN AF: 0.288

Gnomad4 NFE AF: 0.303

Gnomad4 OTH AF: 0.331

Alfa AF: 0.300 Hom.: 9047

Bravo AF: 0.325

Asia WGS AF: 0.387 AC: 1349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.5
DANN	Benign	0.43

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: rs11058197; hg19: chr12-125968344;