rs10773689

chr12-129635581-C-Achr12-129635581-C-T

Variant summary

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

The NM_133448.3(TMEM132D):c.968+64229G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.393 in 152,100 control chromosomes in the GnomAD database, including 11,865 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 0.39 (11865 hom., cov: 33)
• Consequence: TMEM132D NM_133448.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.882

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM132D	NM_133448.3	c.968+64229G>T		intron_variant		ENST00000422113.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM132D	ENST00000422113.7	c.968+64229G>T		intron_variant		1	NM_133448.3	P1

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59736 AN: 151982 Hom.: 11864 Cov.: 33

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.393 AC: 59761 AN: 152100 Hom.: 11865 Cov.: 33 AF XY: 0.392 AC XY: 29112 AN XY: 74360

Gnomad4 AFR AF: 0.365

Gnomad4 AMR AF: 0.417

Gnomad4 ASJ AF: 0.435

Gnomad4 EAS AF: 0.493

Gnomad4 SAS AF: 0.419

Gnomad4 FIN AF: 0.365

Gnomad4 NFE AF: 0.397

Gnomad4 OTH AF: 0.405

Alfa AF: 0.403 Hom.: 11862

Bravo AF: 0.401

Asia WGS AF: 0.434 AC: 1509 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.31
Dann	Benign	0.49

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: rs10773689; hg19: chr12-130120126;