rs12580240

Positions:

• chr12-129162027-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_133448.3(TMEM132D):​c.1443+47493T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0914 in 152,164 control chromosomes in the GnomAD database, including 1,576 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 0.091 (1576 hom., cov: 32)
• Consequence: TMEM132D NM_133448.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0260

Genes affected

TMEM132D (HGNC:29411): (transmembrane protein 132D)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TMEM132D	NM_133448.3	c.1443+47493T>C		intron_variant		ENST00000422113.7	NP_597705.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TMEM132D	ENST00000422113.7	c.1443+47493T>C		intron_variant		1	NM_133448.3	ENSP00000408581.2

Frequencies

GnomAD3 genomes AF: 0.0912 AC: 13873 AN: 152048 Hom.: 1571 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0695

Gnomad ASJ AF: 0.00490

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.0491

Gnomad FIN AF: 0.00367

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0135

Gnomad OTH AF: 0.0666

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

GnomAD4 genome AF: 0.0914 AC: 13914 AN: 152164 Hom.: 1576 Cov.: 32 AF XY: 0.0911 AC XY: 6782 AN XY: 74416

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.0694

Gnomad4 ASJ AF: 0.00490

Gnomad4 EAS AF: 0.144

Gnomad4 SAS AF: 0.0496

Gnomad4 FIN AF: 0.00367

Gnomad4 NFE AF: 0.0135

Gnomad4 OTH AF: 0.0668

Alfa AF: 0.0368 Hom.: 275

Bravo AF: 0.102

Asia WGS AF: 0.0900 AC: 314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.9
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: rs12580240; hg19: chr12-129646572;