rs7296262

Variant names:

• chr12-128610527-T-C
• rs7296262
• NM_001136103.3:c.1122-5625T>C

Your query was ambiguous. Multiple possible variants found:

• chr12-128610527-T-C
• chr12-128610527-T-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.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
• Publications: 11 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=-0.83).
• 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 rank	MANE	Protein	UniProt
TMEM132C	NM_001136103.3	c.1122-5625T>C		intron_variant	Intron 3 of 8	ENST00000435159.3	NP_001129575.2
TMEM132C	NM_001387058.1	c.1062-5625T>C		intron_variant	Intron 3 of 8		NP_001373987.1
TMEM132C	XM_047429886.1	c.1122-5625T>C		intron_variant	Intron 3 of 8		XP_047285842.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM132C	ENST00000435159.3	c.1122-5625T>C		intron_variant	Intron 3 of 8	5	NM_001136103.3	ENSP00000410852.2

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

African (AFR) AF: 0.530 AC: 21792 AN: 41114

American (AMR) AF: 0.472 AC: 7169 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.456 AC: 1574 AN: 3454

East Asian (EAS) AF: 0.383 AC: 1944 AN: 5072

South Asian (SAS) AF: 0.349 AC: 1659 AN: 4754

European-Finnish (FIN) AF: 0.360 AC: 3791 AN: 10522

Middle Eastern (MID) AF: 0.486 AC: 141 AN: 290

European-Non Finnish (NFE) AF: 0.443 AC: 29971 AN: 67606

Other (OTH) AF: 0.480 AC: 1009 AN: 2100

Alfa AF: 0.442 Hom.: 31844

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
PhyloP100		0.65
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: rs7296262; hg19: chr12-129095072;