chr12-128621865-C-G

Variant names:

• chr12-128621865-C-G
• rs953182
• NM_001136103.3:c.1305+5530C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001136103.3(TMEM132C):​c.1305+5530C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 152,154 control chromosomes in the GnomAD database, including 1,000 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 0.11 (1000 hom., cov: 31)
• Consequence: TMEM132C NM_001136103.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.778
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.161 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001136103.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM132C	NM_001136103.3	MANE Select	c.1305+5530C>G		intron	N/A	NP_001129575.2
	TMEM132C	NM_001387058.1		c.1245+5530C>G		intron	N/A	NP_001373987.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM132C	ENST00000435159.3	TSL:5 MANE Select	c.1305+5530C>G		intron	N/A	ENSP00000410852.2

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16576 AN: 152036 Hom.: 1001 Cov.: 31

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.0659

Gnomad ASJ AF: 0.0663

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.0466

Gnomad FIN AF: 0.0960

Gnomad MID AF: 0.0955

Gnomad NFE AF: 0.0931

Gnomad OTH AF: 0.0898

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

GnomAD4 genome AF: 0.109 AC: 16597 AN: 152154 Hom.: 1000 Cov.: 31 AF XY: 0.107 AC XY: 7932 AN XY: 74386

African (AFR) AF: 0.164 AC: 6806 AN: 41506

American (AMR) AF: 0.0659 AC: 1007 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0663 AC: 230 AN: 3470

East Asian (EAS) AF: 0.125 AC: 646 AN: 5152

South Asian (SAS) AF: 0.0464 AC: 224 AN: 4824

European-Finnish (FIN) AF: 0.0960 AC: 1017 AN: 10598

Middle Eastern (MID) AF: 0.0993 AC: 29 AN: 292

European-Non Finnish (NFE) AF: 0.0931 AC: 6332 AN: 68010

Other (OTH) AF: 0.0894 AC: 188 AN: 2104

Alfa AF: 0.111 Hom.: 126

Bravo AF: 0.111

Asia WGS AF: 0.0860 AC: 297 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.3
DANN	Benign	0.77
PhyloP100		0.78
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: rs953182; hg19: chr12-129106410;