12-129745862-G-T

Position:

• chr12-129745862-G-T

Variant summary

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

The NM_133448.3(TMEM132D):​c.80-45164C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.502 in 152,024 control chromosomes in the GnomAD database, including 19,956 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 0.50 (19956 hom., cov: 33)
• Consequence: TMEM132D NM_133448.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.598

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.583 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM132D	NM_133448.3	c.80-45164C>A		intron_variant		ENST00000422113.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM132D	ENST00000422113.7	c.80-45164C>A		intron_variant		1	NM_133448.3	P1

Frequencies

GnomAD3 genomes AF: 0.502 AC: 76290 AN: 151906 Hom.: 19961 Cov.: 33

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.560

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.602

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.502 AC: 76292 AN: 152024 Hom.: 19956 Cov.: 33 AF XY: 0.500 AC XY: 37155 AN XY: 74302

Gnomad4 AFR AF: 0.359

Gnomad4 AMR AF: 0.446

Gnomad4 ASJ AF: 0.560

Gnomad4 EAS AF: 0.448

Gnomad4 SAS AF: 0.495

Gnomad4 FIN AF: 0.602

Gnomad4 NFE AF: 0.588

Gnomad4 OTH AF: 0.525

Alfa AF: 0.558 Hom.: 11842

Bravo AF: 0.481

Asia WGS AF: 0.451 AC: 1569 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.61

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: rs7979367; hg19: chr12-130230407;