12-128360026-T-C

Variant names:

• chr12-128360026-T-C
• rs952093
• NM_001136103.3:c.86-54706T>C

Variant summary

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

The NM_001136103.3(TMEM132C):​c.86-54706T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 152,126 control chromosomes in the GnomAD database, including 1,674 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 0.14 (1674 hom., cov: 32)
• Consequence: TMEM132C NM_001136103.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.13

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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMEM132C	NM_001136103.3	c.86-54706T>C		intron_variant	Intron 1 of 8	ENST00000435159.3	NP_001129575.2
TMEM132C	NM_001387058.1	c.26-54706T>C		intron_variant	Intron 1 of 8		NP_001373987.1
TMEM132C	XM_047429886.1	c.86-54706T>C		intron_variant	Intron 1 of 8		XP_047285842.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM132C	ENST00000435159.3	c.86-54706T>C		intron_variant	Intron 1 of 8	5	NM_001136103.3	ENSP00000410852.2

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21090 AN: 152008 Hom.: 1667 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.0859

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.139 AC: 21117 AN: 152126 Hom.: 1674 Cov.: 32 AF XY: 0.143 AC XY: 10622 AN XY: 74376

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.188

Gnomad4 ASJ AF: 0.0859

Gnomad4 EAS AF: 0.361

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.143

Alfa AF: 0.121 Hom.: 1339

Bravo AF: 0.147

Asia WGS AF: 0.245 AC: 850 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.42
DANN	Benign	0.46

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.16		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: rs952093; hg19: chr12-128844571;