rs2197777

chr12-125346673-T-Cchr12-125346673-T-G

Variant summary

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

The NM_001366854.1(TMEM132B):c.68-2779T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 152,172 control chromosomes in the GnomAD database, including 6,953 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 0.30 (6953 hom., cov: 33)
• Consequence: TMEM132B NM_001366854.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80

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=-0.64).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.413 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM132B	NM_001366854.1	c.68-2779T>C		intron_variant		ENST00000682704.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM132B	ENST00000682704.1	c.68-2779T>C		intron_variant			NM_001366854.1	P2
TMEM132B	ENST00000299308.7	c.53-2779T>C		intron_variant		5		A2
TMEM132B	ENST00000535330.1	n.227-2779T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45229 AN: 152054 Hom.: 6948 Cov.: 33

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.297 AC: 45259 AN: 152172 Hom.: 6953 Cov.: 33 AF XY: 0.296 AC XY: 22015 AN XY: 74400

Gnomad4 AFR AF: 0.265

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.278

Gnomad4 EAS AF: 0.297

Gnomad4 SAS AF: 0.428

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.304

Gnomad4 OTH AF: 0.295

Alfa AF: 0.312 Hom.: 9728

Bravo AF: 0.307

Asia WGS AF: 0.385 AC: 1339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
Cadd	Benign	2.2
Dann	Benign	0.82

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: rs2197777; hg19: chr12-125831219;