chr12-129571259-G-A

Position:

• chr12-129571259-G-A

Variant summary

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

The NM_133448.3(TMEM132D):​c.969-40054C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.392 in 151,942 control chromosomes in the GnomAD database, including 11,798 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 (11798 hom., cov: 32)
• Consequence: TMEM132D NM_133448.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.727

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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TMEM132D	NM_133448.3	c.969-40054C>T		intron_variant		ENST00000422113.7	NP_597705.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TMEM132D	ENST00000422113.7	c.969-40054C>T		intron_variant		1	NM_133448.3	ENSP00000408581	P1

Frequencies

GnomAD3 genomes AF: 0.392 AC: 59444 AN: 151824 Hom.: 11774 Cov.: 32

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.392 AC: 59509 AN: 151942 Hom.: 11798 Cov.: 32 AF XY: 0.391 AC XY: 29026 AN XY: 74232

Gnomad4 AFR AF: 0.371

Gnomad4 AMR AF: 0.483

Gnomad4 ASJ AF: 0.302

Gnomad4 EAS AF: 0.537

Gnomad4 SAS AF: 0.423

Gnomad4 FIN AF: 0.317

Gnomad4 NFE AF: 0.387

Gnomad4 OTH AF: 0.404

Alfa AF: 0.388 Hom.: 10241

Bravo AF: 0.405

Asia WGS AF: 0.497 AC: 1723 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.63
DANN	Benign	0.81

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: rs155697; hg19: chr12-130055804;