rs10773568

Variant names:

• chr12-128701645-G-A
• rs10773568
• NM_001136103.3:c.2122-3445G>A

Variant summary

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

The NM_001136103.3(TMEM132C):​c.2122-3445G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 152,008 control chromosomes in the GnomAD database, including 14,056 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 0.41 (14056 hom., cov: 31)
• Consequence: TMEM132C NM_001136103.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0810
• Publications: 5 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.499 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMEM132C	NM_001136103.3	c.2122-3445G>A		intron_variant	Intron 8 of 8	ENST00000435159.3	NP_001129575.2
TMEM132C	NM_001387058.1	c.2062-3445G>A		intron_variant	Intron 8 of 8		NP_001373987.1
TMEM132C	XM_047429886.1	c.2122-3007G>A		intron_variant	Intron 8 of 8		XP_047285842.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM132C	ENST00000435159.3	c.2122-3445G>A		intron_variant	Intron 8 of 8	5	NM_001136103.3	ENSP00000410852.2

Frequencies

GnomAD3 genomes AF: 0.415 AC: 62974 AN: 151888 Hom.: 14059 Cov.: 31

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.414

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.414 AC: 62988 AN: 152008 Hom.: 14056 Cov.: 31 AF XY: 0.417 AC XY: 30954 AN XY: 74306

African (AFR) AF: 0.241 AC: 9991 AN: 41452

American (AMR) AF: 0.415 AC: 6335 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 1687 AN: 3472

East Asian (EAS) AF: 0.430 AC: 2221 AN: 5162

South Asian (SAS) AF: 0.361 AC: 1742 AN: 4822

European-Finnish (FIN) AF: 0.515 AC: 5439 AN: 10558

Middle Eastern (MID) AF: 0.414 AC: 121 AN: 292

European-Non Finnish (NFE) AF: 0.503 AC: 34193 AN: 67948

Other (OTH) AF: 0.420 AC: 887 AN: 2110

Alfa AF: 0.437 Hom.: 5422

Bravo AF: 0.397

Asia WGS AF: 0.369 AC: 1282 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.38
PhyloP100		0.081
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: rs10773568; hg19: chr12-129186190;