rs7296262

chr12-128610527-T-Cchr12-128610527-T-G

Variant summary

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

The NM_001136103.3(TMEM132C):c.1122-5625T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.46 in 151,020 control chromosomes in the GnomAD database, including 16,028 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 0.46 (16028 hom., cov: 31)
• Consequence: TMEM132C NM_001136103.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.651

Genes affected

TMEM132C (HGNC:25436): (transmembrane protein 132C) 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.524 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM132C	NM_001136103.3	c.1122-5625T>C		intron_variant		ENST00000435159.3
TMEM132C	NM_001387058.1	c.1062-5625T>C		intron_variant
TMEM132C	XM_047429886.1	c.1122-5625T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM132C	ENST00000435159.3	c.1122-5625T>C		intron_variant		5	NM_001136103.3	P1

Frequencies

GnomAD3 genomes AF: 0.460 AC: 69412 AN: 150902 Hom.: 15976 Cov.: 31

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.460 AC: 69530 AN: 151020 Hom.: 16028 Cov.: 31 AF XY: 0.457 AC XY: 33698 AN XY: 73806

Gnomad4 AFR AF: 0.530

Gnomad4 AMR AF: 0.472

Gnomad4 ASJ AF: 0.456

Gnomad4 EAS AF: 0.383

Gnomad4 SAS AF: 0.349

Gnomad4 FIN AF: 0.360

Gnomad4 NFE AF: 0.443

Gnomad4 OTH AF: 0.480

Alfa AF: 0.439 Hom.: 22812

Bravo AF: 0.474

Asia WGS AF: 0.389 AC: 1355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	6.5
Dann	Benign	0.72

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: rs7296262; hg19: chr12-129095072;