NM_001136103.3:c.974+11673A>G

Variant names:

• chr12-128427293-A-G
• rs10773541
• NM_001136103.3:c.974+11673A>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.974+11673A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.627 in 151,836 control chromosomes in the GnomAD database, including 30,029 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 0.63 (30029 hom., cov: 31)
• Consequence: TMEM132C NM_001136103.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08
• Publications: 1 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.704 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.974+11673A>G		intron	N/A	NP_001129575.2
	TMEM132C	NM_001387058.1		c.914+11673A>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.974+11673A>G		intron	N/A	ENSP00000410852.2

Frequencies

GnomAD3 genomes AF: 0.627 AC: 95099 AN: 151718 Hom.: 30000 Cov.: 31

Gnomad AFR AF: 0.589

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.674

Gnomad EAS AF: 0.562

Gnomad SAS AF: 0.724

Gnomad FIN AF: 0.683

Gnomad MID AF: 0.691

Gnomad NFE AF: 0.647

Gnomad OTH AF: 0.625

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

GnomAD4 genome AF: 0.627 AC: 95175 AN: 151836 Hom.: 30029 Cov.: 31 AF XY: 0.627 AC XY: 46553 AN XY: 74200

African (AFR) AF: 0.589 AC: 24384 AN: 41382

American (AMR) AF: 0.584 AC: 8909 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.674 AC: 2335 AN: 3466

East Asian (EAS) AF: 0.562 AC: 2901 AN: 5166

South Asian (SAS) AF: 0.724 AC: 3477 AN: 4802

European-Finnish (FIN) AF: 0.683 AC: 7186 AN: 10514

Middle Eastern (MID) AF: 0.685 AC: 200 AN: 292

European-Non Finnish (NFE) AF: 0.647 AC: 43947 AN: 67952

Other (OTH) AF: 0.626 AC: 1318 AN: 2104

Alfa AF: 0.623 Hom.: 24734

Bravo AF: 0.616

Asia WGS AF: 0.609 AC: 2116 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.19
DANN	Benign	0.44
PhyloP100		-2.1
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: rs10773541; hg19: chr12-128911838;