rs10773568

chr12-128701645-G-A

Variant summary

Our verdict is Benign. Variant got -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

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=-0.9).
• 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/exons	MANE	UniProt
TMEM132C	NM_001136103.3	c.2122-3445G>A		intron_variant		ENST00000435159.3
TMEM132C	NM_001387058.1	c.2062-3445G>A		intron_variant
TMEM132C	XM_047429886.1	c.2122-3007G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM132C	ENST00000435159.3	c.2122-3445G>A		intron_variant		5	NM_001136103.3	P1

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

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.415

Gnomad4 ASJ AF: 0.486

Gnomad4 EAS AF: 0.430

Gnomad4 SAS AF: 0.361

Gnomad4 FIN AF: 0.515

Gnomad4 NFE AF: 0.503

Gnomad4 OTH AF: 0.420

Alfa AF: 0.428 Hom.: 2780

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs10773568; hg19: chr12-129186190;